Transcriptome, proteome, and metabolome reveal the mechanism of tolerance to selenate toxicity in Cardamine violifolia

Overexpression of anthocyanin activator LrAN2 improving black goji berry (Lycium ruthenicum) tolerant to cadmium stress

Plant and soil exposed to heavy metals such as cadmium (Cd) threaten the environment and human health. It remains unknown whether or not MYB-type anthocyanin regulator AN2 play a role in tolerance to Cd stress. In this study, overexpression of Lycium ruthenicum AN2 (OE-LrAN2) enhance transgenic seedlings tolerant to Cd stress, which may contribute to the increased biomass and optimized redox homeostasis through modulating the biosynthesis of antioxidants such as anthocyanin, ascorbate, and carotenoid and the antioxidant enzyme system including CAT, SOD and POD. The OE-LrAN2 seedlings treated with 0, 25, 50, 100 μM CdCl2 for 30d were utilized for transcriptomic analysis. A LrAN2-mediated regulatory network was constructed by weighted gene co-expression network analysis to predict the potential genes involved in L. ruthenicum tolerant to Cd stress. Furthermore, chromatin immunoprecipitation sequencing analysis indicate that LrAN2-targeting genes are associated with the biosynthetic genes related to anthocyanin, glycinebetaine and proline, phytohormone such as auxin, ethylene, and cytokinin, and solute transport including heavy metal cation-transporting ATPase, MATE and ABC transporters. Dual luciferase reporter assay confirm that LrAN2 activate the expression of genes related to carotenoid biosynthesis (LrBCH), MATE-type anthocyanin transporter (LrTT12), and auxin-responsive protein family (LrSAUR72). In vivo functional characterization in yeast confirmed that LrAN2-targeting LrTT12 (TT12Lru03G01504) sequestrate Cd into vacuole and thereby detoxifying Cd stress. Taken together, multi-strategies mediated by LrAN2 improve L. ruthenicum tolerant to Cd stress, which open a novel avenue to cope with the long-term unresolved Cd pollution. The LrAN2-targeting genes identified in this study will be a valuable gene resource to genetically improve crops tolerant to Cd stress.

Selenium: The Toxicant for Pathogen and Pest but the Guardian of Soil and Crop

Selenium (Se) is an essential micronutrient for higher organisms and plays a beneficial role in plant growth and development. In recent years, there has been growing interest in the using of Se to enhance plant resilience, particularly in mitigating the effects of diseases and pests in agricultural systems. This review offers a comprehensive analysis of the sources and chemical forms of Se in soil, investigates the mechanisms of plant uptake and metabolism of different Se forms, and evaluates the physical and chemical inhibition of pathogens by various Se forms, as well as the role of Se in enhancing plant systemic resistance for crop protection. Additionally, we summarize current research on the role of Se in pest and disease control and explore potential future research directions, with a focus on integrating Se into sustainable agricultural practices. The insights presented in this review seek to establish a solid scientific foundation for Se-based approaches to pest control and emphasize its potential application in sustainable agriculture.

Genome-wide identification of MYB gene family and exploration of selenium metabolism-related candidates in paper mulberry (Broussonetia papyrifera)

KEY MESSAGE

Genome-wide identified 144 MYB family members in B. papyrifera. Integrated correlation analysis and target gene-binding motif prediction indicate that BpMYB135 is vital in regulating selenium metabolism. Selenium is an essential micronutrient for maintaining the health of humans and animals. Broussonetia papyrifera, a forage tree with high nutritional value, exhibits a remarkable ability to accumulate selenium. Although previous studies have preliminarily unfolded the molecular mechanisms underlying selenium accumulation, the roles of transcription factors in regulating selenium uptake and transformation remain poorly understood. This study used various strategies including bioinformatic, physiological, and molecular experiments to explore candidates regarding Se metabolism. Briefly, 144 MYB transcription factor family members were identified and classified into four types (R1, R2R3, R1R2R3, and R4), with phylogenetic analysis further dividing them into 58 subfamilies. The promoters of those BpMYBs contain numerous cis-acting elements associated with plant growth, development, and stress response. qRT-PCR assay confirmed 8 of 15 BpMYBs exhibit a remarkable correlation with selenium content at the threshold absolute value of 0.5. Additionally, foliar application of exogenous abscisic acid (ABA), methyl jasmonate (MeJA), and salicylic acid (SA) reveals different response patterns of BpMYBs. The subcellular localization assay simultaneously verifies that the candidate BpMYB135 functions within the nucleus. Overall, this funding highlights the potential regulatory mechanisms of selenium metabolism in B. papyrifera, providing a foundation for improving its forage value through genetic modification.

Physiological and Transcriptome Analysis Provide Insights into the Effects of Low and High Selenium on Methionine and Starch Metabolism in Rice Seedlings

Selenium (Se) is an essential micronutrient for the human body and is closely linked to health. Rice (Oryza sativa L.), as a major staple food globally, is the primary source of Se intake for humans. To better achieve Se biofortification in rice, it is crucial to understand the molecular mechanisms behind rice's response to different Se concentrations. This study investigates the morphological and transcriptomic responses of rice seedlings to low (1 µM, LSe) and high (10 µM, HSe) Se concentrations compared to a control (CK). Morphological analyses revealed that LSe promoted growth, enhancing shoot and root length and biomass, whereas HSe treatment inhibited these parameters, indicating Se's dual role in rice growth. Notably, the most significant promotion of rice growth was observed at the Se concentration of 1 µM. The organic Se content and antioxidant enzyme activities (SOD, POD and CAT) in rice seedlings also reached their maximum values simultaneously. Total RNA was extracted for transcriptome sequencing, and differential gene expression analysis was conducted using DESeq2. Transcriptomic sequencing highlighted distinct responses under LSe and HSe conditions. Gene ontology (GO) enrichment analysis revealed significant involvement in processes related to oxidoreductase activity and cellular structures. KEGG pathway analysis emphasized that Se treatments notably enhanced the glutathione metabolism pathway, which is crucial for antioxidant defense. Additionally, significant changes were observed in starch and sucrose metabolism and cysteine (Cys) and methionine (Met) metabolism pathways, showing upregulation under LSe treatment and downregulation under HSe. Six key genes were validated using qRT-PCR, confirming their differential expression under varied Se treatments. The Cys, Met and starch content assays as well as qRT-PCR data demonstrated that LSe promoted the synthesis and accumulation of Cys, Met and starch, supporting enhanced growth and antioxidant capacity. Conversely, HSe inhibited the synthesis and accumulation of Cys, Met and starch in rice seedlings, and these data were also consistent with the physiological phenotype. These findings provide insights into the molecular mechanisms by which rice seedlings adapt to varying Se levels, with implications for Se biofortification and stress management strategies in crops.

Mitigation of aluminum toxicity in rice seedlings using biofabricated selenium nanoparticles and nitric oxide: Synergistic effects on oxidative stress tolerance and sulfur metabolism

Biofabricated selenium nanoparticles (Se-NPs) and sodium nitroprusside-derived nitric oxide (NO) singly or in combination was evaluated to improve tolerance to aluminum (Al) stress in rice (Oryza sativa L. cv. Swarna Sub1). The major objective was to elucidate contribution of sulfur reduction processes in oxidative stress tolerance along with cellular responses. Rice seedlings were primed against Al stress (550 μM) by the exogenous application of 100 μM NO and 20 ppm Se-NPs synthesized from a Salvinia molesta D. Mitch. extract. Green-synthesized Se-NPs (∼67 nm) had a crystalline, amorphous structure, high stability with functional groups in capping agents. The seedlings reduced bioaccumulation of Al in root tissues under SNP, Se-NPs, and in combination. Bioexclusion of Al was done in endodermal tissues by callose formation and binding in a fluorescent complex in the root tips. An upregulation of sulfur metabolism, including total sulfur, cysteine, cysteine synthase, and ATP sulfurylase activity was modulated by SNP + Se-NPs combination. Oxidative stress inducing metal stress for membrane oxidation into malondialdehyde, superoxide radical, and hydrogen peroxide, were also moderated by the SNP + Se-NPs combination. The Al-induced oxidative stress was relieved by a proportionate increase in superoxide dismutase and peroxidase activity. A higher ratio of ascorbate to dehydroascorbate and reduced to oxidized glutathione induced by the SNP + Se-NPs combination was supported antioxidation. These findings may substantiate the efficiency of green-synthesized Se-NPs together with SNP (as an NO donor) for amelioration of Al hazardous in crops like rice.

Exogenous selenium enhances cadmium stress tolerance by improving physiological characteristics of Artemisia argyi seedlings

The contamination of Chinese medicinal materials with cadmium (Cd) is a pressing global issue that poses significant risks to human health. The beneficial effects of selenium (Se) have been established in improving plant growth and reducing Cd accumulation in plant under Cd stress. This study employed soil cultivation experiments to investigate the remediation effects of exogenous Se (0, 0.5, 1, and 2 mg kg⁻1) under varying levels of Cd stress (0, 0.6 and 4 mg kg⁻1). The findings revealed that Cd stress markedly impaired seedling growth, biomass, and physiological characteristics in Artemisia argyi. Regardless of Cd levels, exogenous Se significantly enhanced seedling biomass, improved antioxidant enzyme activity, and increased the plant's antioxidant capacity, thereby mitigating Cd stress. Additionally, exogenous Se promoted A. argyi plant growth, decreased malondialdehyde (MDA) content in the shoots, and under two Cd stress environments of 0.6 and 4 mg kg⁻1, the application of 1 mg kg⁻1 Se reduced the Cd content in the aboveground parts of seedlings by 31.99 and 82.21%, respectively. We conclude 1 mg kg⁻1 Se could represent a promising strategy to contribute to the development and sustainability of crop production on soils contaminated with Cd at a concentration of up to 0.6 and 4 mg kg⁻1. These results indicate that exogenous Se activates physiological and biochemical defense mechanisms in A. argyi seedlings against Cd stress, offering a foundation for cultivating high-yield, high-quality A. argyi in Cd-contaminated soils.

Overlapping Transcriptome Alterations Reveal the Mechanism of Interaction between Selenium and Zinc and Their Common Effect on Essential Nutrient Metabolism in Mung Bean (Vigna radiata L.)

Selenium (Se) and zinc (Zn) deficiencies have become serious global food security and public health problems. Biofortification through foliar fertilizer is a nonspecific, low-tech, and cost-effective strategy. Se and Zn have overlapping physiological roles and interacting relationships in plants. Mung bean is superior for Se enrichment and an excellent Zn carrier. However, the molecular mechanism underlying the interaction between Se and Zn in the mung bean remains unclear. Herein, Se and Zn accumulation, antioxidant activities, physiological determination, and transcriptomic analysis were performed under both Se and Zn treatments. Common essential roles of Se and Zn in mung bean were reflected by the comprehensively altered ten physiological indexes under both Se2 (24 g·ha-1) and Zn1 (1.2 kg·ha-1) treatments. Overlapping transcriptome changes and common DEGs in two compared groups revealed that the upregulated expression of sulfate transporters (SULTRs), phosphate transporters (PHTs), and Zinc-regulated/Iron-regulated-like protein (ZIP) family genes under Se and Zn treatments directly promoted both Se and Zn intakes. Furthermore, the altered Se/Sulfur, nitrogen, and carbohydrate metabolisms are closely interlinked with the uptake and assimilation of Se and Zn via the 20 key genes that we filtered through the protein-protein interaction (PPI) network analysis. Further analysis indicated that l-methionine γ-lyase (E 4.4.1.11) genes may play an important role in the transamination of selenomethionine and its derivatives; glutamine synthetase (GS), nitrate reductase (NR), and starch synthase (SS) genes may regulate the nitrogen assimilation and carbohydrate metabolism, which provide more carriers for Se and Zn; glutathione peroxidase (GPx), glutamate-cysteine ligase catalytic subunit (GCLC), and serine acetyltransferase (SAT) genes may accelerate the GSH-GSSH cycle and promote Se and Zn storages. This study provides new molecular insights into the comprehensive improvement of the nutritional quality of mung beans in Se and Zn biofortification productions.

Novel selenium-enriched Pichia kudriavzevii as a dietary supplement to alleviate dextran sulfate sodium-induced colitis in mice by modulating the gut microbiota and host metabolism

Inflammatory bowel disease (IBD) poses persistent challenges due to its chronic and recurrent nature, exacerbated by the unsatisfactory outcomes of the traditional treatment approaches. In this study, we developed a dietary supplement, selenium-enriched Pichia kudriavzevii (SeY), to alleviate dextran sulfate sodium-induced colitis in mice. The newly developed functional food shows dual-functional activity, acting both as a probiotic and a reliable source of organic selenium. This study aimed to investigate the preventive effects of SeY against dextran sulfate sodium-induced colitis in mice and elucidate the underlying mechanisms. Results showed that SeY, especially at high doses (HSeY), significantly ameliorated colitis symptoms, reduced colonic damage, attenuated inflammatory responses, and mitigated oxidative stress. Furthermore, HSeY strengthened intestinal barrier function by increasing goblet cell numbers, upregulating MUC2 expression, and enhancing tight junction proteins (ZO-1, claudin-1, and occludin). Additionally, HSeY alleviated gut microbiota dysbiosis by promoting the colonization of beneficial bacteria such as norank-f-Muribaculaceae and Bacteroides, while suppressing harmful microorganisms such as norank-f-norank-o-Clostridia-UCG-014. The altered gut microbiota also affected gut metabolism, with differential metabolites primarily associated with amino acids, such as tryptophan metabolism, contributing to the mitigation of oxidative stress and inflammatory responses. Further studies involving antibiotic-mediated depletion of gut flora and fecal microbiota transfer trials corroborated that the preventive effect of HSeY against IBD relied on the gut microbiota. This study provides vital insights into colitis prevention and advances selenium-enriched fortified food-targeted nutritional interventions.

Recovery of Selenium-Enriched Polysaccharides from Cardamine violifolia Residues: Comparison on Structure and Antioxidant Activity by Different Extraction Methods

The residues from selenium-enriched Cardamine violifolia after the extraction of protein were still rich in polysaccharides. Thus, the recovery of selenium polysaccharides (SePSs) was compared using hot water extraction and ultrasonic-assisted extraction techniques. The yield, extraction rate, purity, specific energy consumption, and content of total and organic selenium from different SePS extracts were determined. The results indicated that at conditions of 250 W (ultrasonic power), 30 °C, and a liquid-to-material ratio of 30:1 extracted for 60 min, the yield of SePSs was 3.97 ± 0.07%, the extraction rate was 22.76 ± 0.40%, and the purity was 65.56 ± 0.35%, while the total and organic selenium content was 749.16 ± 6.91 mg/kg and 628.37 ± 5.93 mg/kg, respectively. Compared to traditional hot water extraction, ultrasonic-assisted extraction significantly improves efficiency, reduces energy use, and boosts both total and organic selenium content in the extract. Measurements of particle size, molecular weight, and monosaccharide composition, along with infrared and ultraviolet spectroscopy, revealed that ultrasonic-assisted extraction breaks down long-chain structures, decreases particle size, and changes monosaccharide composition in SePSs, leading to lower molecular weight and reduced dispersity. The unique structure of SePSs, which integrates selenium with polysaccharide groups, results in markedly improved antioxidant activity and reducing power, even at low concentrations, due to the synergistic effects of selenium and polysaccharides. This study establishes a basis for using SePSs in functional foods.

Identification, characterization, and expression analysis of WRKY transcription factors in Cardamine violifolia reveal the key genes involved in regulating selenium accumulation

BACKGROUND

Cardamine violifolia is a significant Brassicaceae plant known for its high selenium (Se) accumulation capacity, serving as an essential source of Se for both humans and animals. WRKY transcription factors play crucial roles in plant responses to various biotic and abiotic stresses, including cadmium stress, iron deficiency, and Se tolerance. However, the molecular mechanism of CvWRKY in Se accumulation is not completely clear.

RESULTS

In this study, 120 WRKYs with conserved domains were identified from C. violifolia and classified into three groups based on phylogenetic relationships, with Group II further subdivided into five subgroups. Gene structure analysis revealed WRKY variations and mutations within the CvWRKYs. Segmental duplication events were identified as the primary driving force behind the expansion of the CvWRKY family, with numerous stress-responsive cis-acting elements found in the promoters of CvWRKYs. Transcriptome analysis of plants treated with exogenous Se and determination of Se levels revealed a strong positive correlation between the expression levels of CvWRKY034 and the Se content. Moreover, CvWRKY021 and CvWRKY099 exhibited high homology with AtWRKY47, a gene involved in regulating Se accumulation in Arabidopsis thaliana. The WRKY domains of CvWRKY021 and AtWRKY47 were highly conserved, and transcriptome data analysis revealed that CvWRKY021 responded to Na2SeO4 induction, showing a positive correlation with the concentration of Na2SeO4 treatment. Under the induction of Na2SeO3, CvWRKY021 and CvWRKY034 were significantly upregulated in the roots but downregulated in the shoots, and the Se content in the roots increased significantly and was mainly concentrated in the roots. CvWRKY021 and CvWRKY034 may be involved in the accumulation of Se in roots.

CONCLUSIONS

The results of this study elucidate the evolution of CvWRKYs in the C. violifolia genome and provide valuable resources for further understanding the functional characteristics of WRKYs related to Se hyperaccumulation in C. violifolia.

Unveiling the vital role of soil microorganisms in selenium cycling: a review

Selenium (Se) is a vital trace element integral to numerous biological processes in both plants and animals, with significant impacts on soil health and ecosystem stability. This review explores how soil microorganisms facilitate Se transformations through reduction, oxidation, methylation, and demethylation processes, thereby influencing the bioavailability and ecological functions of Se. The microbial reduction of Se compounds, particularly the conversion of selenate and selenite to elemental Se nanoparticles (SeNPs), enhances Se assimilation by plants and impacts soil productivity. Key microbial taxa, including bacteria such as Pseudomonas and Bacillus, exhibit diverse mechanisms for Se reduction and play a substantial role in the global Se cycle. Understanding these microbial processes is essential for advancing soil management practices and improving ecosystem health. This review underscores the intricate interactions between Se and soil microorganisms, emphasizing their significance in maintaining ecological balance and promoting sustainable agricultural practices.

Selenite improves growth by modulating phytohormone pathways and reprogramming primary and secondary metabolism in tomato plants

Selenium (Se) is an essential micronutrient in organisms that has a significant impact on physiological activity and gene expression in plants, thereby affecting growth and development. Humans and animals acquire Se from plants. Tomato (Solanum lycopersicum L.) is an important vegetable crop worldwide. Improving the Se nutrient level not only is beneficial for growth, development and stress resistance in tomato plants but also contributes to improving human health. However, the molecular basis of Se-mediated tomato plant growth has not been fully elucidated. In this study, using physiological and transcriptomic analyses, we investigated the effects of a low dosage of selenite [Se(Ⅳ)] on tomato seedling growth. Se(IV) enhanced the photosynthetic efficiency and increased the accumulation of soluble sugars, dry matter and organic matter, thereby promoting tomato plant growth. Transcriptome analysis revealed that Se(IV) reprogrammed primary and secondary metabolic pathways, thus modulating plant growth. Se(IV) also increased the concentrations of auxin, jasmonic acid and salicylic acid in leaves and the concentration of cytokinin in roots, thus altering phytohormone signaling pathways and affecting plant growth and stress resistance in tomato plants. Furthermore, exogenous Se(IV) alters the expression of genes involved in flavonoid biosynthesis, thereby modulating plant growth and development in tomato plants. Taken together, these findings provide important insights into the regulatory mechanisms of low-dose Se(IV) on tomato growth and contribute to the breeding of Se-accumulating tomato cultivars.

Multi-omics integration analysis reveals the molecular mechanisms of drought adaptation in homologous tetraploid alfalfa(Medicago sativa 'Xinjiang-Daye')

Drought stress is a predominant abiotic factor leading to decreased alfalfa yield. Genomic ploidy differences contribute to varying adaptation mechanisms of different alfalfa cultivars to drought conditions. This study employed a multi-omics approach to characterize the molecular basis of drought tolerance in a tetraploid variant of alfalfa (Medicago sativa, Xinjiang-Daye). Under drought treatment, a total of 4446 genes, 859 proteins, and 524 metabolites showed significant differences in abundance. Integrative analysis of the multi-omics data revealed that regulatory modules involved in flavonoid biosynthesis, plant hormone signalling transduction, linoleic acid metabolism, and amino acid biosynthesis play crucial roles in alfalfa adaptation to drought stress. The severity of drought led to the substantial accumulation of flavonoids, plant hormones, free fatty acids, amino acids, and their derivatives in the leaves. Genes such as PAL, 4CL, CHI, CHS, PP2C, ARF_3, and AHP_4 play pivotal regulatory roles in flavonoid biosynthesis and hormone signalling pathways. Differential expression of the LOX gene emerged as a key factor in the elevated levels of free fatty acids. Upregulation of P5CS_1 and GOT1/2 contributed significantly to the accumulation of Pro and Phe contents. ERF19 emerged as a principal positive regulator governing the synthesis of the aforementioned compounds. Furthermore, observations suggest that Xinjiang-Daye alfalfa may exhibit widespread post-transcriptional regulatory mechanisms in adapting to drought stress. The study findings unveil the critical mechanisms by which Xinjiang-Daye alfalfa adapts to drought stress, offering novel insights for the improvement of alfalfa germplasm resources.

Multi-omics analysis of Populus simonii × P. nigra leaves under Hyphantria cunea stress

Poplar is an important greening and timber tree species in China, which has great economic and ecological values. However, the spread of Hyphantria cunea has become increasingly serious in recent years, resulting in huge economic loss of poplar production. Exploring the molecular mechanism of poplar reponse to H. cunea stress has significant implications for future development of new insect-resistant poplar varieties using genetic engineering technology. In this study, a total of 1039 differentially expressed genes (DEGs), 106 differentially expressed proteins (DEPs) and 212 differentially expressed metabolites (DEMs) were screened from Populus simonii × P. nigra leaves under H. cunea stress by transcriptome, proteomics and metabolomics analysis, respectively. GO and KEGG analysis showed that the DEGs and DEPs are associated with endopeptidase inhibitor activity, stress response, α-linolenic acid metabolism, phenylpropanoid biosynthesis and metabolic pathways, cysteine and methionine metabolism pathways and MAKP signaling pathway. Metabolomics analysis showed the most of DEMs were lipids and lipid molecules, and the pathways associated with transcriptome mainly include plant hormone signal transduction, α-linolenic acid metabolic pathway, amino sugar and nucleotide sugar metabolism, and phenylpropanoid biosynthesis. In particular, multi-omics analysis showed that several pathways such as α-linolenic acid metabolic, phenylpropanoid biosynthesis and metabolic pathway and cysteine and methionine metabolic pathway were significantly enriched in the three omics, which may play an important role in the resistance to pests in poplar.

Physiological and multi-omics analysis reveals the influence of copper on Halophila beccarii Asch

High concentrations of copper can pollute coastal waters, primarily from agricultural runoff and mining activities, which can harm marine organisms, including seagrasses. The molecular mechanism of copper toxicity to seagrass currently remains unclear. To determine the response to copper, physiological and multi-omic analyses were conducted to explore the molecular mechanism by which copper affects the global threatened seagrass Halophila beccarii Asch. Excessive copper stress causes oxidative damage and stimulates the activity of the antioxidant enzyme system to remove excess reactive oxygen species (ROS), thereby reducing the damage caused by copper stress. Cu increases the activities of superoxide dismutase (EC 1.15.1.1), catalase (EC 1.11.1.6), peroxidase (EC 1.11.1.7), ascorbate peroxidase (EC 1.11.1.11), glutathione peroxidase (EC 1.11.1.9), ascorbate oxidase (EC 1.10.3.3), glutathione reductase (EC 1.6.4.2), and dehydroascorbate reductase (EC 1.8.5.1) and the content of malondialdehyde and reduces the activity of monodehydroascorbate reductase (EC 1.6.5.4). Under copper stress, H. beccarii upregulates the metabolic pathways of steroid biosynthesis and cutin, suberin, and wax biosynthesis, downregulates the metabolic pathways of arginine and proline metabolism and fructose and mannose metabolism; the levels of expression of the ribosome-related genes; upregulates the levels of expression of circadian rhythm-related proteins and downregulates the levels of glutathione metabolism and the proteins related to carbon fixation. This study provides new insights into the response of seagrass to copper stress and reports potential candidate metabolites, genes, and proteins that can be considered as biomarkers to improve the protection and management of seagrass meadows.

The Performance and Evolutionary Mechanism of Ganoderma lucidum in Enhancing Selenite Tolerance and Bioaccumulation

BACKGROUND

Selenium (Se) pollution poses serious threats to terrestrial ecosystems. Mushrooms are important sources of Se with the potential for bioremediation. Pre-eminent Se resources must possess the ability to tolerate high levels of Se. To obtain Se-accumulating fungi, we isolated selenite-tolerance-enhanced Ganoderma lucidum JNUSE-200 through adaptive evolution.

METHODS

The molecular mechanism responsible for selenite tolerance and accumulation was explored in G. lucidum JNUSE-200 by comparing it with the original strain, G. lucidum CGMCC 5.26, using a combination of physiological and transcriptomic approaches.

RESULTS

G. lucidum JNUSE-200 demonstrated tolerance to 200 mg/kg selenite in liquid culture and exhibited normal growth, whereas G. lucidum CGMCC 5.26 experienced reduced growth, red coloration, and an unpleasant odor as a result of exposure to selenite at the same concentration. In this study, G. lucidum JNUSE-200 developed a triple defense mechanism against high-level selenite toxicity, and the key genes responsible for improved selenite tolerance were identified.

CONCLUSIONS

The present study offers novel insights into the molecular responses of fungi towards selenite, providing theoretical guidance for the breeding and cultivation of Se-accumulating varieties. Moreover, it significantly enhances the capacity of the bio-manufacturing industry and contributes to the development of beneficial applications in environmental biotechnology through fungal selenite transformation bioprocesses.

Identification and functional characterization of ABC transporters for selenium accumulation and tolerance in soybean

ATP-binding cassette (ABC) transporters were crucial for various physiological processes like nutrition, development, and environmental interactions. Selenium (Se) is an essential micronutrient for humans, and its role in plants depends on applied dosage. ABC transporters are considered to participate in Se translocation in plants, but detailed studies in soybean are still lacking. We identified 196 ABC genes in soybean transcriptome under Se exposure using next-generation sequencing and single-molecule real-time sequencing technology. These proteins fell into eight subfamilies: 8 GmABCA, 51 GmABCB, 39 GmABCC, 5 GmABCD, 1 GmABCE, 10 GmABCF, 74 GmABCG, and 8 GmABCI, with amino acid length 121-3022 aa, molecular weight 13.50-341.04 kDa, and isoelectric point 4.06-9.82. We predicted a total of 15 motifs, some of which were specific to certain subfamilies (especially GmABCB, GmABCC, and GmABCG). We also found predicted alternative splicing in GmABCs: 60 events in selenium nanoparticles (SeNPs)-treated, 37 in sodium selenite (Na2SeO3)-treated samples. The GmABC genes showed differential expression in leaves and roots under different application of Se species and Se levels, most of which are belonged to GmABCB, GmABCC, and GmABCG subfamilies with functions in auxin transport, barrier formation, and detoxification. Protein-protein interaction and weighted gene co-expression network analysis suggested functional gene networks with hub ABC genes, contributing to our understanding of their biological functions. Our results illuminate the contributions of GmABC genes to Se accumulation and tolerance in soybean and provide insight for a better understanding of their roles in soybean as well as in other plants.

Comprehensive physiology and proteomics analysis revealed the molecular toxicological mechanism of Se stress on indica and japonica rice

Selenium pollution can lead to a decrease in crop yield and quality. However, the toxicological mechanisms of high Se concentrations on crops remain unclear. This study aimed to elucidate the physiological and proteomic molecular responses to Se stress in Oryza sativa. The results showed that under selenium stress, enzymatic activities of catalase, peroxidase, and superoxide dismutase in indica rice decreased by 61%, 28%, and 68%, respectively. The contents of non-enzymatic antioxidant substances ascorbic acid, glutathione, cysteine, proline, anthocyanidin, and flavonoids were decreased by 13%, 39%, 46%, 32%, 20%, and 5%, respectively, which significantly inhibited the antioxidant stress process of plants. At the same time, the results of proteomics analysis showed that rice seedlings, under Se stress, are involved in photosynthesis, photosynthesis-antenna proteins, carbon fixation, porphyrin metabolism, glyoxylate, and dicarboxylate. The differentially expressed proteins in metabolism and glutathione metabolism pathways showed a downward trend. It significantly inhibited the anti-oxidative stress, photosynthesis, and energy cycling process in plant cells, destroyed the homeostasis balance of rice plants, and inhibited the growth and development of rice. This finding reveals the molecular toxicological mechanism of Se stress on rice seedlings and provides a possible way to improve Se-resistant rice seedlings.

Multi-pathways-mediated mechanisms of selenite reduction and elemental selenium nanoparticles biogenesis in the yeast-like fungus Aureobasidium melanogenum I15

Selenium (Se) plays a critical role in diverse biological processes and is widely used across manufacturing industries. However, the contamination of Se oxyanions also poses a major public health concern. Microbial transformation is a promising approach to detoxify Se oxyanions and produce elemental selenium nanoparticles (SeNPs) with versatile industrial potential. Yeast-like fungi are an important group of environmental microorganisms, but their mechanisms for Se oxyanions reduction remain unknown. In this study, we found that Aureobasidium melanogenum I15 can reduce 1.0 mM selenite by over 90% within 48 h and efficiently form intracellular or extracellular spherical SeNPs. Metabolomic and proteomic analyses disclosed that A. melanogenum I15 evolves a complicated selenite reduction mechanism involving multiple metabolic pathways, including the glutathione/glutathione reductase pathway, the thioredoxin/thioredoxin reductase pathway, the siderophore-mediated pathway, and multiple oxidoreductase-mediated pathways. This study provides the first report on the mechanism of selenite reduction and SeNPs biogenesis in yeast-like fungi and paves an alternative avenue for the bioremediation of selenite contamination and the production of functional organic selenium compounds.

Utilizing transcriptomics and proteomics to unravel key genes and proteins of Oryza sativa seedlings mediated by selenium in response to cadmium stress

BACKGROUND

Cadmium (Cd) pollution has declined crop yields and quality. Selenium (Se) is a beneficial mineral element that protects plants from oxidative damage, thereby improving crop tolerance to heavy metals. The molecular mechanism of Se-induced Cd tolerance in rice (Oryza sativa) is not yet understood. This study aimed to elucidate the beneficial mechanism of Se (1 mg/kg) in alleviating Cd toxicity in rice seedlings.

RESULTS

Exogenous selenium addition significantly improved the toxic effect of cadmium stress on rice seedlings, increasing plant height and fresh weight by 20.53% and 34.48%, respectively, and increasing chlorophyll and carotenoid content by 16.68% and 15.26%, respectively. Moreover, the MDA, ·OH, and protein carbonyl levels induced by cadmium stress were reduced by 47.65%, 67.57%, and 56.43%, respectively. Cell wall metabolism, energy cycling, and enzymatic and non-enzymatic antioxidant systems in rice seedlings were significantly enhanced. Transcriptome analysis showed that the expressions of key functional genes psbQ, psbO, psaG, psaD, atpG, and PetH were significantly up-regulated under low-concentration Se treatment, which enhanced the energy metabolism process of photosystem I and photosystem II in rice seedlings. At the same time, the up-regulation of LHCA, LHCB family, and C4H1, PRX, and atp6 functional genes improved the ability of photon capture and heavy metal ion binding in plants. Combined with proteome analysis, the expression of functional proteins OsGSTF1, OsGSTU11, OsG6PDH4, OsDHAB1, CP29, and CabE was significantly up-regulated under Se, which enhanced photosynthesis and anti-oxidative stress mechanism in rice seedlings. At the same time, it regulates the plant hormone signal transduction pathway. It up-regulates the expression response process of IAA, ABA, and JAZ to activate the synergistic effect between each cell rapidly and jointly maintain the homeostasis balance.

CONCLUSION

Our results revealed the regulation process of Se-mediated critical metabolic pathways, functional genes, and proteins in rice under cadmium stress. They provided insights into the expression rules and dynamic response process of the Se-mediated plant resistance mechanism. This study provided the theoretical basis and technical support for crop safety in cropland ecosystems and cadmium-contaminated areas.

Selenium in plants: A nexus of growth, antioxidants, and phytohormones

Selenium (Se) is an essential micronutrient for both human and animals. Plants serve as the primary source of Se in the food chain. Se concentration and availability in plants is influenced by soil properties and environmental conditions. Optimal Se levels promote plant growth and enhance stress tolerance, while excessive Se concentration can result in toxicity. Se enhances plants ROS scavenging ability by promoting antioxidant compound synthesis. The ability of Se to maintain redox balance depends upon ROS compounds, stress conditions and Se application rate. Furthermore, Se-dependent antioxidant compound synthesis is critically reliant on plant macro and micro nutritional status. As these nutrients are fundamental for different co-factors and amino acid synthesis. Additionally, phytohormones also interact with Se to promote plant growth. Hence, utilization of phytohormones and modified crop nutrition can improve Se-dependent crop growth and plant stress tolerance. This review aims to explore the assimilation of Se into plant proteins, its intricate effect on plant redox status, and the specific interactions between Se and phytohormones. Furthermore, we highlight the proposed physiological and genetic mechanisms underlying Se-mediated phytohormone-dependent plant growth modulation and identified research opportunities that could contribute to sustainable agricultural production in the future.

How plants respond to heavy metal contamination: a narrative review of proteomic studies and phytoremediation applications

MAIN CONCLUSION

Heavy metal pollution caused by human activities is a serious threat to the environment and human health. Plants have evolved sophisticated defence systems to deal with heavy metal stress, with proteins and enzymes serving as critical intercepting agents for heavy metal toxicity reduction. Proteomics continues to be effective in identifying markers associated with stress response and metabolic processes. This review explores the complex interactions between heavy metal pollution and plant physiology, with an emphasis on proteomic and biotechnological perspectives. Over the last century, accelerated industrialization, agriculture activities, energy production, and urbanization have established a constant need for natural resources, resulting in environmental degradation. The widespread buildup of heavy metals in ecosystems as a result of human activity is especially concerning. Although some heavy metals are required by organisms in trace amounts, high concentrations pose serious risks to the ecosystem and human health. As immobile organisms, plants are directly exposed to heavy metal contamination, prompting the development of robust defence mechanisms. Proteomics has been used to understand how plants react to heavy metal stress. The development of proteomic techniques offers promising opportunities to improve plant tolerance to toxicity from heavy metals. Additionally, there is substantial scope for phytoremediation, a sustainable method that uses plants to extract, sequester, or eliminate contaminants in the context of changes in protein expression and total protein behaviour. Changes in proteins and enzymatic activities have been highlighted to illuminate the complex effects of heavy metal pollution on plant metabolism, and how proteomic research has revealed the plant's ability to mitigate heavy metal toxicity by intercepting vital nutrients, organic substances, and/or microorganisms.

Transcriptome and co-expression network revealed molecular mechanism underlying selenium response of foxtail millet (Setaria italica)

Introduction

Selenium-enriched foxtail millet (Setaria italica) represents a functional cereal with significant health benefits for humans. This study endeavors to examine the impact of foliar application of sodium selenite (Na2SeO4) on foxtail millet, specifically focusing on selenium (Se) accumulation and transportation within various plant tissues.

Methods

To unravel the molecular mechanisms governing selenium accumulation and transportation in foxtail millet, we conducted a comprehensive analysis of selenium content and transcriptome responses in foxtail millet spikelets across different days (3, 5, 7, and 12) under Na2SeO4 treatment (200 μmol/L).

Results

Foxtail millet subjected to selenium fertilizer exhibited significantly elevated selenium levels in each tissue compared to the untreated control. Selenate was observed to be transported and accumulated sequentially in the leaf, stem, and spikes. Transcriptome analysis unveiled a substantial upregulation in the transcription levels of genes associated with selenium metabolism and transport, including sulfate, phosphate, and nitrate transporters, ABC transporters, antioxidants, phytohormone signaling, and transcription factors. These genes demonstrated intricate interactions, both synergistic and antagonistic, forming a complex network that regulated selenate transport mechanisms. Gene co-expression network analysis highlighted three transcription factors in the tan module and three transporters in the turquoise module that significantly correlated with selenium accumulation and transportation. Expression of sulfate transporters (SiSULTR1.2b and SiSULTR3.1a), phosphate transporter (PHT1.3), nitrate transporter 1 (NRT1.1B), glutathione S-transferase genes (GSTs), and ABC transporter (ABCC13) increased with SeO4 2- accumulation. Transcription factors MYB, WRKY, and bHLH were also identified as players in selenium accumulation.

Conclusion

This study provides preliminary insights into the mechanisms of selenium accumulation and transportation in foxtail millet. The findings hold theoretical significance for the cultivation of selenium-enriched foxtail millet.

Selenium speciation and volatile flavor compound profiles in the edible flowers, stems, and leaves of selenium-hyperaccumulating vegetable Cardamine violifolia

Cardamine violifolia is a unique selenium (Se)-hyperaccumulating vegetable in China. The total Se content and Se speciation of three edible parts, including flowers, stems, and leaves were detected by HPLC-ICP-MS. Volatile organic compounds (VOCs) greatly impact food flavor. The VOCs of three samples were analyzed by E-nose, HS-GC-IMS, and HS-SPME-GC-MS. The results showed that the total Se content in flowers was significantly higher than that in leaves and was the lowest in stems. Organic Se accounts for more than 98% of the total Se content, primarily selenocystine, followed by methyl selenocysteine. A total of 102 VOCs were identified from C. violifolia, mainly esters, aldehydes, alcohols, and ketones. Flowers contained abundant VOCs, while stems and leaves contained fewer but similar profiles. Moreover, multivariate statistical analysis was applied to investigate the VOC variations and marker VOCs. This work can provide useful knowledge for understanding the Se characteristics and flavor of C. violifolia.

Selenate triggers diverse oxidative responses in Astragalus species with diverse selenium tolerance and hyperaccumulation capacity

Selenium (Se) hyperaccumulators are capable of uptake and tolerate high Se dosages. Excess Se-induced oxidative responses were compared in Astragalus bisulcatus and Astragalus cicer. Plants were grown on media supplemented with 0, 25 or 75 μM selenate for 14 days. Both A. bisulcatus and A. cicer accumulated >2000 μg/g dry weight Se to the shoot but the translocation factors of A. cicer were below 1 suggesting its non hyperaccumulator nature. A. cicer showed Se sensitivity indicated by reduced seedling fresh weight, root growth and root apical meristem viability, altered element homeostasis in the presence of Se. In Se-exposed A. bisulcatus, less toxic organic Se forms (mainly MetSeCys, γ-Glu-MetSeCys, and a selenosugar) dominated, while these were absent from A. cicer suggesting that the majority of the accumulated Se may be present as inorganic forms. The glutathione-dependent processes were more affected, while ascorbate levels were not notably influenced by Se in either species. Exogenous Se triggered more intense accumulation of malondialdehyde in the sensitive A. cicer compared with the tolerant A. bisulcatus. The extent of protein carbonylation in the roots of the 75 μM Se-exposed A. cicer exceeded that of A. bisulcatus indicating a correlation between selenate sensitivity and the degree of protein carbonylation. Overall, our results reveal connection between oxidative processes and Se sensitivity/tolerance/hyperaccumulation and contribute to the understanding of the molecular responses to excess Se.

Selenium hyperaccumulator plant Cardamine enshiensis: from discovery to application

Selenium (Se) is an essential trace element for animals and humans. Se biofortification and Se functional agriculture are emerging strategies to satisfy the needs of people who are deficient in Se. With 200 km2 of Se-excess area, Enshi is known as the "world capital of Se." Cardamine enshiensis (C. enshiensis) is a Se hyperaccumulation plant discovered in the Se mine drainage area of Enshi. It is edible and has been approved by National Health Commission of the People's Republic of China as a new source of food, and the annual output value of the Se-rich industry in Enshi City exceeds 60 billion RMB. This review will mainly focus on the discovery and mechanism underlying Se tolerance and Se hyperaccumulation in C. enshiensis and highlight its potential utilization in Se biofortification agriculture, graziery, and human health.

Transcriptome and physiological determination reveal the effects of selenite on the growth and selenium metabolism in mung bean sprouts

Selenium (Se) biofortification of crops has been studied to substantially improve the Se content in human dietary food intake. In the present study, Vigna radiata (mung bean) seeds were soaked in different concentrations of sodium selenite (Na₂SeO₃). Low concentration of selenite is conducive to seed germination and growth, and can increase the fresh weight (FW) and dry weight (DW) of sprouts. The concentration of Na₂SeO₃ lower than 50 mg/kg resulted in noticeable elongation in the stem and marginal elongation in root. Mung bean seeds soaked with 80 mg/kg Na₂SeO₃ accounted for 93.77% of organic Se after growing for about 5 days. Transcriptome data revealed that Se treatment enhances starch and sugar metabolism, along with the up-regulation of ribosomal protein and DNA synthesis related genes. Further analysis indicated that the mung bean seeds absorbed Na₂SeO₃ through PHT1.1 and NIP2. Se (IV) was transformed into Se (VI) and transported to stems, leaves and roots through cotyledons during the germination of bean sprouts. SULTR3;3 may play an important role in the transit process. Se (VI) or Se (IV) transported to the leaves was catalytically transformed into SeCys through SiR and CS, and SeCys is further converted to MeSeCys through SMT. Most SeCys were transformed into SeHCys through CBL, transported to plastids, and finally transformed into SeMet through Met Synthase.

Multiomics reveals Claroideoglomus etunicatum regulates plant hormone signal transduction, photosynthesis and La compartmentalization in maize to promote growth under La stress

Rare earth elements (REEs) have been widely used in traditional and high-tech fields, and high doses of REEs are considered a risk to the ecosystem. Although the influence of arbuscular mycorrhizal fungi (AMF) in promoting host resistance to heavy metal (HM) stress has been well documented, the molecular mechanism by which AMF symbiosis enhances plant tolerance to REEs is still unclear. A pot experiment was conducted to investigate the molecular mechanism by which the AMF Claroideoglomus etunicatum promotes maize (Zea mays) seedling tolerance to lanthanum (La) stress (100 mg·kg^-1 La). C. etunicatum symbiosis significantly improved maize seedling growth, P and La uptake and photosynthesis. Transcriptome, proteome, and metabolome analyses performed alone and together revealed that differentially expressed genes (DEGs) related to auxin /indole-3-acetic acid (AUX/IAA) and the DEGs and differentially expressed proteins (DEPs) related to ATP-binding cassette (ABC) transporters, natural resistance-associated macrophage proteins (Nramp6), vacuoles and vesicles were upregulated. In contrast, photosynthesis-related DEGs and DEPs were downregulated, and 1-phosphatidyl-1D-myo-inositol 3-phosphate (PI(3)P) was more abundant under C. etunicatum symbiosis. C. etunicatum symbiosis can promote plant growth by increasing P uptake, regulating plant hormone signal transduction, photosynthesis and glycerophospholipid metabolism pathways and enhancing La transport and compartmentalization in vacuoles and vesicles. The results provide new insights into the promotion of plant REE tolerance by AMF symbiosis and the possibility of utilizing AMF-maize interactions in REE phytoremediation and recycling.

Metabolomics and transcriptomics strategies to reveal the mechanism of diversity of maize kernel color and quality

BACKGROUND

Maize has many kernel colors, from white to dark black. However, research on the color and nutritional quality of the different varieties is limited. The color of the maize grain is an important characteristic. Colored maize is rich in nutrients, which have received attention for their role in diet-related chronic diseases and have different degrees of anti-stress protection for animal and human health.

METHODS

A comprehensive metabolome (LC-MS/MS) and transcriptome analysis was performed in this study to compare different colored maize varieties from the perspective of multiple recombination in order to study the nutritional value of maize with different colors and the molecular mechanism of color formation.

RESULTS

Maize kernels with diverse colors contain different types of health-promoting compounds, highlighting that different maize varieties can be used as functional foods according to human needs. Among them, red-purple and purple-black maize contain more flavonoids than white and yellow kernels. Purple-black kernels have a high content of amino acids and nucleotides, while red-purple kernels significantly accumulate sugar alcohols and lipids.

CONCLUSION

Our study can provide insights for improving people's diets and provide a theoretical basis for the study of food structure for chronic diseases.

Morphophysiological, proteomic and metabolomic analyses reveal cadmium tolerance mechanism in common wheat (Triticum aestivum L.)

Soil cadmium (Cd) contamination can reduce wheat yield and quality, thus threatening food security and human health. Herein, morphological physiology, Cd accumulation and distribution, proteomic and metabolomic analyses were performed (using wheat cultivars 'Luomai23' (LM, Cd-sensitive) and 'Zhongyu10' (ZY, Cd-tolerant) at the seedling stage with sand culture) to reveal Cd tolerance mechanism. Cd inhibited wheat growth, caused oxidative stress, hindered carbon and nitrogen metabolism, and altered the quantity and composition of root exudates. The root Cd concentration was lower in ZY than in LM by about 35% under 15 μM Cd treatments. ZY reduced Cd uptake through root exudation of amino acids and alkaloids. ZY also reduced Cd accumulation through specific up-regulation (twice) of major facilitator superfamily (MFS) proteins. Furthermore, ZY enhanced Cd cell wall fixation and vacuolar compartmentalization by increasing pectin contents, hemicellulose1 contents, and adenosine triphosphate binding cassette subfamily C member 1 (ABCC1) transporter expression, thus reducing the Cd organelle fraction of ZY by about 12% and 44% in root and shoot, respectively, compared with LM. Additionally, ZY had enhanced resilience to Cd due to increased antioxidant capacity, plasma membrane stability, nitrogen metabolism, and endoplasmic reticulum homeostasis, indicating that the increased Cd tolerance could be because of multi-level coordination. These findings provide a reference for exploring the molecular mechanism of Cd tolerance and accumulation, providing a basis for safe utilization of Cd-contaminated soil by breeding Cd-tolerant and low Cd-accumulating wheat varieties.

Pivotal biological processes and proteins for selenite reduction and methylation in Ganoderma lucidum

Microbial transformations, especially the reduction and methylation of Se oxyanion, have gained significance in recent years as effective detoxification methods. Ganoderma lucidum is a typical Se enrichment resource that can reduce selenite to elemental Se and volatile Se metabolites under high selenite conditions. However, the detailed biological processes and reduction mechanisms are unclear. In this study, G. lucidum reduced selenite to elemental Se and further aggregated it into Se nanoparticles with a diameter of < 200 nm, simultaneously accompanied by the production of pungent, odorous, and volatile methyl-selenium metabolites. Tandem mass tag-based quantitative proteomic analysis revealed thioredoxin 1, thioredoxin reductase (NADPH), glutathione reductase, 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase, and cystathionine gamma-lyase as proteins involved in selenite reduction and methylation. Furthermore, the high expression of proteins associated with cell structures that prompted cell lysis may have facilitated Se release. The upregulation of proteins involved in the defense reactions was also detected, reflecting their roles in the self-defense mechanism. This study provides novel insights into the vital role of G. lucidum in mediating Se transformation in the biogeochemical Se cycle and contributes to the application of fungi in Se bioremediation.

Spatial Metallomics Reveals Preferable Accumulation of Methylated Selenium in a Single Seed of the Hyperaccumulator Cardamine violifolia†

Cardamine violifolia is a Se hyperaccumulator found in Enshi, China. In this study, spatial metallomics was applied to visualize the distribution and speciation of Se in a single seed of C. violifolia. It was found that Se reached 1729.89 ± 28.14 mg/kg and the main Se species were SeCys and SeMet in bulk seeds. Further in situ study on a single seed found that the methylated Se species located mostly in the episperm. This is the first visualized evidence of the in situ distribution of methylated Se species in the seeds of C. violifolia. In all, spatial metallomics finds a preferable accumulation of methylated Se species in the seed coat, which deepens the understanding of the tolerance of Se by C. violifolia. The protocol applied in this study may also be used for the understanding of the tolerance of heavy metals/metalloids in other hyperaccumulators.

Integrated transcriptome and metabolome analysis reveals the mechanism of tolerance to manganese and cadmium toxicity in the Mn/Cd hyperaccumulator Celosia argentea Linn

Understanding the molecular mechanism of tolerance to heavy metals in hyperaccumulators is important for improving the efficiency of phytoremediation and is interesting for evolutionary studies on plant adaption to abiotic stress. Celosia argentea Linn. was recently discovered to hyperaccumulate both manganese (Mn) and cadmium (Cd). However, the molecular mechanisms underlying Mn and Cd detoxification in C. argentea are poorly understood. Laboratory studies were conducted using C. argentea seedlings exposed to 360 μM Mn and 8.9 μM Cd hydroponic solutions. Plant leaves were analyzed using transcriptional and metabolomic techniques. A total of 3960 differentially expressed genes (DEGs) in plants were identified under Cd stress, among which 17 were associated with metal transport, and 10 belonged to the ATP transporter families. Exposures to Mn or Cd led to the differential expression of three metal transport genes (HMA3, ABCC15, and ATPase 4). In addition, 33 and 77 differentially expressed metabolites (DEMs) were identified under Mn and Cd stresses, respectively. Metabolic pathway analysis showed that the ABC transporter pathway was the most affected in Mn/Cd exposed seedlings. Conjoint transcriptome and metabolome analysis showed that the glutathione (GSH) metabolic pathway was over-represented in the KEGG pathway of both DEGs and DEMs. Our results confirm that the ABC transporter and GSH metabolic pathways play important roles in Mn and Cd detoxification. These findings provide new insight into the molecular mechanisms of tolerance to Mn and Cd toxicity in plants.

Effect of Nano-Selenium on Nutritional Quality of Cowpea and Response of ABCC Transporter Family

It is an important way for healthy Selenium (Se) supplement to transform exogenous Se into organic Se through crops. In the present study, Vigna unguiculata was selected as a test material and sprayed with biological nano selenium (SeNPs) and Na₂SeO₃, and its nutrient composition, antioxidant capacity, total Se and organic Se content were determined, respectively. Further, the response of ABC transporter family members in cowpea to different exogenous Se treatments was analyzed by transcriptome sequencing combined with different Se forms. The results show that the soluble protein content of cowpea increased after twice Se treatment. SeNPs treatment increased the content of cellulose in cowpea pods. Na₂SeO₃ treatment increased the content of vitamin C (Vc) in cowpea pods. Se treatments could significantly increase the activities of Peroxidase (POD), polyphenol oxidase (PPO) and catalase (CAT) in cowpea pods and effectively maintain the activity of Superoxide dismutase (SOD). SeNPs can reduce the content of malondialdehyde (MDA) in pods. After Se treatment, cowpea pods showed a dose-effect relationship on the absorption and accumulation of total Se, and Na₂SeO₃ treatment had a better effect on the increase of total Se content in cowpea pods. After treatment with SeNPs and Na₂SeO₃, the Se species detected in cowpea pods was mainly SeMet, followed by MeSeCys. Inorganic Se can only be detected in the high concentration treatment group. Analysis of transcriptome data of cowpea treated with Se showed that ABC transporters could play an active role in response to Se stress and Se absorption, among which ABCB, ABCC and ABCG subfamilies played a major role in Se absorption and transportation in cowpea. Further analysis by weighted gene co-expression network analysis (WGCNA) showed that the content of organic Se in cowpea treated with high concentration of SeNPs was significantly and positively correlated with the expression level of three transporters ABCC11, ABCC13 and ABCC10, which means that the ABCC subfamily may be more involved in the transmembrane transport of organic Se in cells.

Microbial functional communities and the antibiotic resistome profile in a high-selenium ecosystem

Enshi City, in the Hubei Province of China, is known as the world capital of selenium with the most abundant selenium resource. An important selenium hyperaccumulator plant, Cardamine violifolia, was found to naturally grow in this high-selenium ecosystem. However, relatively little is known about the impact of the selenium levels on microbial community and functional shifts in C. violifolia rhizosphere. Here, we tested the hypothesis that underground microbial diversity and function vary along a selenium gradient, including antibiotic resistance genes (ARGs). Comprehensive metagenomic analyses, such as taxonomic investigation, functional detection, and ARG annotation, showed that selenium, mercury, cadmium, lead, arsenic, and available phosphorus and potassium were correlated with microbial diversity and function. Thaumarchaeota was exclusively dominant in the highest selenium concentration of mine outcrop, and Rhodanobacter and Nitrospira were predominant in the high-selenium ecosystem. The plant C. violifolia enriched a high concentration of selenium in the rhizosphere compared to those in the bulk soil, and it recruited Variovorax and Polaromonas in its rhizosphere. Microbial abundance showed a trend of increasing first and then decreasing from low to high selenium concentrations. Annotation of ARGs showed that the multidrug resistance genes adeF, mtrA, and poxtA, the aminoglycoside resistance gene rpsL, and the sulfonamide resistant gene sul2 were enriched in the high-selenium system. It was discovered that putative antibiotic resistant bacteria displayed obvious differences in the farmland and the soils with various selenium concentrations, indicating that a high-selenium ecosystem harbors the specific microbes with a higher capacity to enrich or resist selenium, toxic metals, or antibiotics. Taken together, these results reveal the effects of selenium concentration and the selenium hyperaccumulator plant C. violifolia on shaping the microbial functional community and ARGs. Metalloid selenium-inducible antibiotic resistance is worth paying attention to in future.

Transcriptomics and Lipid Metabolomics Analysis of Subcutaneous, Visceral, and Abdominal Adipose Tissues of Beef Cattle

Fat deposition traits are influenced by genetics and environment, which affect meat quality, growth rate, and energy metabolism of domestic animals. However, at present, the molecular mechanism of fat deposition is not entirely understood in beef cattle. Therefore, the current study conducted transcriptomics and lipid metabolomics analysis of subcutaneous, visceral, and abdominal adipose tissue (SAT, VAT, and AAT) of Huaxi cattle to investigate the differences among these adipose tissues and systematically explore how candidate genes interact with metabolites to affect fat deposition. These results demonstrated that compared with SAT, the gene expression patterns and metabolite contents of VAT and AAT were more consistent. Particularly, SCD expression, monounsaturated fatty acid (MUFA) and triglyceride (TG) content were higher in SAT, whereas PCK1 expression and the contents of saturated fatty acid (SFA), diacylglycerol (DG), and lysoglycerophosphocholine (LPC) were higher in VAT. Notably, in contrast to PCK1, 10 candidates including SCD, ELOVL6, ACACA, and FABP7 were identified to affect fat deposition through positively regulating MUFA and TG, and negatively regulating SFA, DG, and LPC. These findings uncovered novel gene resources and offered a theoretical basis for future investigation of fat deposition in beef cattle.

Interaction between selenium and essential micronutrient elements in plants: A systematic review

Nutrient imbalance (i.e., deficiency and toxicity) of microelements is an outstanding environmental issue that influences each aspect of ecosystems. Although the crucial roles of microelements in entire lifecycle of plants have been widely acknowledged, the effective control of microelements is still neglected due to the narrow safe margins. Selenium (Se) is an essential element for humans and animals. Although it is not believed to be indispensable for plants, many literatures have reported the significance of Se in terms of the uptake, accumulation, and detoxification of essential microelements in plants. However, most papers only concerned on the antagonistic effect of Se on metal elements in plants and ignored the underlying mechanisms. There is still a lack of systematic review articles to summarize the comprehensive knowledge on the connections between Se and microelements in plants. In this review, we conclude the bidirectional effects of Se on micronutrients in plants, including iron, zinc, copper, manganese, nickel, molybdenum, sodium, chlorine, and boron. The regulatory mechanisms of Se on these micronutrients are also analyzed. Moreover, we further emphasize the role of Se in alleviating element toxicity and adjusting the concentration of micronutrients in plants by altering the soil conditions (e.g., adsorption, pH, and organic matter), promoting microbial activity, participating in vital physiological and metabolic processes, generating element competition, stimulating metal chelation, organelle compartmentalization, and sequestration, improving the antioxidant defense system, and controlling related genes involved in transportation and tolerance. Based on the current understanding of the interaction between Se and these essential elements, future directions for research are suggested.

Comparative physiological and transcriptome analysis reveals the potential mechanism of selenium accumulation and tolerance to selenate toxicity of Broussonetia papyrifera

Broussonetia papyrifera is an important fodder tree that is widely distributed in China. Enhancing the selenium (Se) content in B. papyrifera may help to improve the nutritional value of the feed. In this study, sodium selenite and selenate were foliar applied to investigate the mechanisms of Se tolerance and accumulation in B. papyrifera. The results showed that both Se forms significantly increased the total Se content, and the proportion of organic Se was significantly higher in the sodium selenite treatment than in the control. In addition, the soluble sugar, phenolic acid and flavonoid contents and antioxidant enzyme activities were increased by exogenous Se. The de novo RNA sequencing results showed that 644 and 1804 differentially expressed genes were identified in the selenite and selenate comparison groups, respectively. Pathway enrichment analysis demonstrated that 24 of the 108 pathways were significantly enriched, of which sulfur assimilation genes in the sodium selenite-treated groups were upregulated, whereas Se conjugation and transporter genes, such as SBP1, PCS, GSTs, ABCs and GPX, were significantly induced under selenate treatment. The hub genes identified by weighted-gene co-expression network analysis further confirmed that sulfur assimilation, conjugation and transporter genes might play a vital role in Se assimilation and tolerance. From this, a model of Se metabolism in B. papyrifera was proposed based on the above physiological and RNA sequencing data. This study is the first study to report that B. papyrifera has a strong ability to accumulate and tolerate exogenous Se, thereby providing a foundation for further characterization of the accumulation and tolerance mechanism of B. papyrifera. Our findings can provide technical support for producing Se-enriched fodder.

The Integral Boosting Effect of Selenium on the Secondary Metabolism of Higher Plants

Selenium is a micronutrient with a wide range of functions in animals, including humans, and in microorganisms such as microalgae. However, its role in plant metabolism remains ambiguous. Recent studies of Se supplementation showed that not only does it increase the content of the element itself, but also affects the accumulation of secondary metabolites in plants. The purpose of this review is to analyze and summarize the available data on the place of selenium in the secondary metabolism of plants and its effect on the accumulation of some plant metabolites (S- and N-containing secondary metabolites, terpenes, and phenolic compounds). In addition, possible molecular mechanisms and metabolic pathways underlying these effects are discussed. It should be noted that available data on the effect of Se on the accumulation of secondary metabolites are inconsistent and contradictory. According to some studies, selenium has a positive effect on the accumulation of certain metabolites, while other similar studies show a negative effect or no effect at all. The following aspects were identified as possible ways of regulating plant secondary metabolism by Se-supplementation: changes occurring in primary S/N metabolism, hormonal regulation, redox metabolism, as well as at the transcriptomic level of secondary metabolite biosynthesis. In all likelihood, the confusion in the results can be explained by other, more complex regulatory mechanisms in which selenium is involved and which affect the production of metabolites. Further study on the involvement of various forms of selenium in metabolic and signaling pathways is crucial for a deeper understanding of its role in growth, development, and health of plants, as well as the regulatory mechanisms behind them.

Dual RNA and 16S ribosomal DNA sequencing reveal arbuscular mycorrhizal fungi-mediated mitigation of selenate stress in Zea mays L. and reshaping of soil microbiota

Excessively high concentrations of selenium (Se) in soil are toxic to crop plants, and inoculation with arbuscular mycorrhizal fungi (AMF) can reverse Se stress in maize (Zea mays L.). To investigate the underlying mechanisms, maize seedlings were treated with sodium selenate (5 mg Se[VI] kg^-1) and/or AMF (Funneliformis mosseae and Claroideoglomus etunicatum). Dual RNA sequencing in mycorrhiza and 16 S ribosomal DNA sequencing in soil were performed. The results showed that Se(VI) application alone decreased plant dry weight, but increased plant Se concentration, total Se content (mainly selenocysteine), and root superoxide content. Inoculation with either F. mosseae or C. etunicatum increased plant dry weight, decreased Se accumulation and selenocysteine proportion, enhanced root peroxidase activity, and alleviated oxidative stress in Se(VI)-treated plants. Inoculation also downregulated the expression of genes encoding Se transporters, assimilation enzymes, and cysteine-rich receptor-like kinases in Se(VI)-stressed plants, similar to plant-pathogen interaction and glutathione metabolism related genes. Conversely, genes encoding selenium-binding proteins and those related to phenylpropanoid biosynthesis were upregulated in inoculated plants under Se(VI) stress. Compared with Se(VI)-free plants, Se tolerance index, symbiotic feedback percentage on plant dry weight, and root colonization rate were all increased in inoculated plants under Se(VI) stress, corresponding to upregulated expression of 'key genes' in symbiosis. AMF inoculation increased bacterial diversity, decreased the relative abundances of selenobacteria related to plant Se absorption (e.g., Proteobacteria and Firmicutes), and improved bacterial network complexity in Se(VI)-stressed soils. We suggest that stress-mediated enhancement of mycorrhizal symbiosis contributed to plant Se(VI) tolerance, whereas AMF-mediated reshaping of soil bacterial community structure prevented excessive Se accumulation in maize.

Comprehensive proteomic and metabolomic analysis uncover the response of okra to drought stress

The response of okra to drought stress is very complicated, and the molecular mechanisms underlying this process remains ambiguous up to now. In this study, different degrees of water-stress responses of okra leaf were explained by using transcriptomics and metabolomic approaches. The photosynthesis and glycometabolism in okra leaf were both adversely affected by drought stress, leading to inhibition of the carbohydrate metabolic process, and then influencing the secondary plant metabolism. Further, drought stress disturbed amino acid metabolism, especially for the tyrosine-derived pathway as well as arginine and proline metabolism, which have been shown to be significantly enriched under water withholding conditions based on multi-omics conjoint analysis (transcriptome, proteome and metabolome). In-depth analysis of the internal linkages between differentially expressed transcripts, proteins, and metabolites decidedly indicate that tyrosine metabolism could confer tolerance to drought stress by influencing carbon and nitrogen metabolism. These findings provide a whole framework of the regulation and relationships of major transcripts and peptides related to secondary metabolism, particularly, the role of critical proteins and metabolite involved in the change of amino acid metabolism in response to drought stress.

Integration of transcriptomic and proteomic analyses of Rhododendron chrysanthum Pall. in response to cold stress in the Changbai Mountains

BACKGROUND

Cold stress is one of the abiotic stresses that affect plant growth and development, as well as life and geographical distribution important. For researching how plants react to low temperature stress, Rhododendron chrysanthum Pall. (R. chrysanthum) growing in Changbai Mountains of China is an essential study subject.

METHODS AND RESULTS

R. chrysanthum was cold-treated at 4 °C for 12 h (cold-stress group-CS, and controls-CK), combined with transcriptomics (RNA-seq) and proteomics (iTRAQ) techniques, to investigate the response mechanisms of R. chrysanthum response to cold stress. Cold stress resulted in the discovery of 12,261 differentially expressed genes (DEGs) and 360 differentially expressed proteins (DEPs). Correlation of proteomic and transcriptome data, proteome regulation of distinct subcellular localization, and gene/protein functional groupings are all part of the investigation.

CONCLUSIONS

The combined analysis showed that 6378 DEPs matched the corresponding DEGs when the control was compared with the cold-treated samples (CK vs CS). The analysis identified 54 DEGs-DEPs associated with cold stress. cold-tolerant DEGs-DEPs were enriched with hydrolase activity, acting on glycosyl bonds, carbon-oxygen lyase activity and ferric iron binding. Seven potential DEGs-DEPs with significant involvement in the cold stress response were identified by co-expression network analysis. These findings identify the synergistic effect of DEGs-DEPs as the key to improve the cold tolerance of R. chrysanthum and provide a theoretical basis for further studies on its cold resistance subsequently.

Advances in Research on the Involvement of Selenium in Regulating Plant Ecosystems

Selenium is an essential trace element which plays an important role in human immune regulation and disease prevention. Plants absorb inorganic selenium (selenite or selenate) from the soil and convert it into various organic selenides (such as seleno amino acids, selenoproteins, and volatile selenides) via the sulfur metabolic pathway. These organic selenides are important sources of dietary selenium supplementation for humans. Organoselenides can promote plant growth, improve nutritional quality, and play an important regulatory function in plant ecosystems. The release of selenium-containing compounds into the soil by Se hyperaccumulators can promote the growth of Se accumulators but inhibit the growth and distribution of non-Se accumulators. Volatile selenides with specific odors have a deterrent effect on herbivores, reducing their feeding on plants. Soil microorganisms can effectively promote the uptake and transformation of selenium in plants, and organic selenides in plants can improve the tolerance of plants to pathogenic bacteria. Although selenium is not an essential trace element for plants, the right amount of selenium has important physiological and ecological benefits for them. This review summarizes recent research related to the functions of selenium in plant ecosystems to provide a deeper understanding of the significance of this element in plant physiology and ecosystems and to serve as a theoretical basis and technical support for the full exploitation and rational application of the ecological functions of selenium-accumulating plants.

Insights into growth-promoting effect of nanomaterials: Using transcriptomics and metabolomics to reveal the molecular mechanisms of MWCNTs in enhancing hyperaccumulator under heavy metal(loid)s stress

Carbon nanotubes present potential applications in soil remediation, particularly in phytoremediation. Yet, how multi-walled carbon nanotubes (MWCNTs) induced hyperaccumulator growth at molecular level remains unclear. Here, physio-biochemical, transcriptomic, and metabolomic analyses were performed to determine the effect of MWCNTs on Solanum nigrum L. (S. nigrum) growth under cadmium and arsenic stresses. 500 mg/kg MWCNTs application significantly promoted S. nigrum growth, especially for root tissues. Specially, MWCNTs application yields 1.38-fold, 1.56-fold, and 1.37-fold enhancement in the shoot length, root length, and fresh biomass, respectively. Furthermore, MWCNTs significantly strengthened P and Fe absorption in roots, as well as the activities of antioxidative enzymes. Importantly, the transcriptomic analysis indicated that S. nigrum gene expression was sensitive to MWCNTs, and MWCNTs upregulated advantageous biological processes under heavy metal(loid)s stress. Besides, MWCNTs reprogramed metabolism that related to defense system, leading to accumulation of 4-hydroxyphenylpyruvic acid (amino acid), 4-hydroxycinnamic acid (xenobiotic), and (S)-abscisic acid (lipid). In addition, key common pathways of differentially expressed metabolites and genes, including "tyrosine metabolism" and "isoquinoline alkaloid biosynthesis" were selected via integrating transcriptome and metabolome analyses. Combined omics technologies, our findings provide molecular mechanisms of MWCNTs in promoting S. nigrum growth, and highlight potential application of MWCNTs in soil remediation.

A new selenium source from Se-enriched Cardamine violifolia improves growth performance, anti-oxidative capacity and meat quality in broilers

Background

Cardamine violifolia (Cv) is a kind of selenium-enriched plant which contains high levels of organic selenium (Se) such as selenocysteine and methylselenocysteine. This study was conducted to investigate the effects of this new source of Se on the growth performance, anti-oxidative capacity and meat quality in broilers compared with other frequently-used Se sources.

Methods

A total of 240 broilers were allotted into 4 treatments: (1) Control group (Se free diets, CON); (2) Sodium selenite group (0.3 mg/kg Se sourced from Na2SeO3 diets, SeNa); (3) Selenium yeast group (0.3 mg/kg Se sourced from Se-Yeast diets, SeY); (4) Plant Se group (0.3 mg/kg Se sourced from Cv diets, SeCv). The whole study lasted 42 days and was divided into 2 stages (1-21 d as earlier stage and 22-42 d as later stage).

Results

The results showed that the broilers fed SeCv diets had improved average daily gain and the ratio of feed to gain compared to the broilers fed SeNa and SeY diets during the earlier stage. However, there was no significant difference in growth performance of broilers fed these 3 sources of Se diets during the whole period. The broilers fed SeCv diets had improved intestinal mucosal morphology on d 21 and 42. Enhanced liver total anti-oxidative capacity was observed from the broilers fed SeCv diets compared with the other 2 Se sources diets on d 21. Furthermore, lower liver malondialdehyde contents were determined from the broilers fed SeCv and SeY diets compared with SeNa diets. At last, the broilers fed SeCv had increased redness in thigh muscle and decreased cooking loss in both breast and thigh muscle compared with the boilers fed SeNa diets. However, the broilers had similar meat quality between SeCv group and SeY group.

Conclusion

In conclusion, these results demonstrated that SeCv was a well-organic Se source for broilers.

Multi-omics analysis reveals the influence of tetracycline on the growth of ryegrass root

Environmental factors, including antibiotics such as tetracycline, can alter biological processes in plants. To ascertain how cell/tissue response to tetracycline, a multi-omic analysis was implemented to explore the molecular mechanism of tetracycline influencing the growth of ryegrass root. Tetracycline induced extensive changes in the root metabolome in plants, particularly impacting metabolites of flavonoid metabolic pathways, which were supported through consistent differences between transcriptome and proteome. Cross-comparison between mRNA and protein contents considered the authentication of congruence with related metabolites and revealed changes of several biological processes under tetracycline stress. Overall, we present an undemanding multi-omic strategy to survey the significant influence on the root under tetracycline stress.

Transcriptomic and metabolomic investigation of metabolic disruption in Vigna unguiculata L. triggered by acetamiprid and cyromazine

A variety of pesticides are often used in agricultural management to control target pests but may trigger disruptions in the metabolism of nontarget organisms, ultimately affecting crop quality. Acetamiprid (ACE) and cyromazine (CYR) are two frequently used insecticides on cowpea, so it is critical to understand whether these two insecticides cause metabolic disorders in cowpea quality changes and the mechanism by which they do so. Here, we used metabolomic and transcriptomic methods to explore the mechanisms of the effects of ACE, CYR, and their mixture (MIX) on cowpea. In this study, ACE, CYR and MIX had no significant effects on plant biomass or growth status but decreased the contents of starch, soluble protein, and total flavonoids. All treatments reduced the total flavonoid content, but MIX showed the largest reduction of 10.02%. Metabolomic and transcriptomic analyses revealed that ACE markedly affected amino acid metabolism, and CYR and MIX affected sugar metabolism and flavonoid synthesis pathways. ACE and CYR reduced the levels of alanine, glutamic acid, isoleucine and phenylalanine and the expression of amino acid-related genes in cowpea, while MIX significantly increased the levels of most amino acids. All pesticide treatments reduced saccharide levels and related genes, with the most pronounced reduction in the MIX treatment. Exposure to ACE decreased the content of naringenin chalcone and quercetin and increased the content of anthocyanins in cowpeas, while MIX caused a significant decrease in the contents of quercetin and anthocyanins. According to the current study, single and mixed pesticides had different effects on the active ingredients of cowpea, with MIX causing the most significant decrease in the metabolite content of cowpea. These results provide important insights from a molecular perspective on how neonicotinoids and triazine insecticides affect cowpea metabolism.

Comparative study of the effects of selenium yeast and sodium selenite on selenium content and nutrient quality in broccoli florets (Brassica oleracea L. var. italica)

BACKGROUND

Approximately 0.5-1 billion people worldwide face the risk of selenium (Se) deficiency because of the low Se concentration in their diets. Broccoli can accumulate Se and comprises a source of daily Se supplement for humans. Se biofortification is an effective strategy for enhancing Se content in crops. In the present study, the effects of Se yeast and selenite application on the Se content and nutrient quality of broccoli were investigated.

RESULTS

Broccoli growth was promoted by Se yeast but inhibited by selenite. The total Se content of broccoli florets remarkably increased with increasing exogenous Se fertilizer concentrations. The main Se species in broccoli florets were methyl-selenocysteine and selenomethionine, and their contents were significantly higher under Se yeast treatments than under selenite treatments. Se(VI) was detected only under selenite treatments. Se yeast and selenite had different influences on soluble sugar, soluble protein, vitamin C and free amino acid contents in broccoli florets. The total phenolic acid and glucosinolate contents were substantially increased by Se yeast and selenite, although the total flavonoid content was reduced by Se yeast. Tests on antioxidant enzyme activities revealed that several antioxidant enzymes (catalase, peroxidase, superoxide dismutase and glutathione peroxidase) responded to Se yeast and selenite treatments.

CONCLUSION

Se yeast is preferred over selenite for maximizing Se uptake and nutrient accumulation in Se-rich broccoli cultivation. However, an extremely high Se content in broccoli florets cannot be directly consumed by humans, although they can be processed into Se supplements. © 2021 Society of Chemical Industry.

Multi-Approach Analysis Reveals Pathways of Cold Tolerance Divergence in Camellia japonica

Understanding the molecular mechanism of the cold response is critical to improve horticultural plant cold tolerance. Here, we documented the physiological, transcriptome, proteome, and hormonal dynamics to cold stress in temperate genotype (Tg) and subtropical genotype (Sg) populations of Camellia japonica. Tg C. japonica suffered minimal osmotic and oxidative damage compared to Sg C. japonica under the same cold treatment. Transcriptional and translational differences increased under the cold treatment, indicating that Tg C. japonica was affected by the environment and displayed both conserved and divergent mechanisms. About 60% of the genes responding to cold had similar dynamics in the two populations, but 1,896 transcripts and 455 proteins differentially accumulated in response to the cold between Tg and Sg C. japonica. Co-expression analysis showed that the ribosomal protein and genes related to photosynthesis were upregulated in Tg C. japonica, and tryptophan, phenylpropanoid, and flavonoid metabolism were regulated differently between the two populations under cold stress. The divergence of these genes reflected a difference in cold responsiveness. In addition, the decrease in the abscisic acid (ABA)/gibberellic acid (GA) ratio regulated by biosynthetic signal transduction pathway enhanced cold resistance in Tg C. japonica, suggesting that hormones may regulate the difference in cold responsiveness. These results provide a new understanding of the molecular mechanism of cold stress and will improve cold tolerance in horticultural plants.