Expression profiles of Arabidopsis thaliana in mineral deficiencies reveal novel transporters involved in metal homeostasis

NtZIP5A/B is involved in the regulation of Zn/Cu/Fe/Mn/Cd homeostasis in tobacco

Plants grow in soils with varying concentrations of microelements, often in the presence of toxic metals e.g. Cd. To cope, they developed molecular mechanisms to regulate metal cross-homeostasis. Understanding underlying complex relationships is key to improving crop productivity. Recent research suggests that the Zn and Cd uptake protein NtZIP5A/B [Zinc-regulated, Iron-regulated transporter-like Proteins (ZIPs)] from tobacco (Nicotiana tabacum L. v. Xanthi) is involved in the regulation of a cross-talk between the two metals. Here, we support this conclusion by showing that RNAi-mediated silencing of NtZIP5A/B resulted in a reduction of Zn accumulation and that this effect was significantly enhanced by the presence of Cd. Our data also point to involvement of NtZIP5B in regulating a cross-talk between Cu, Fe, and Mn. Using yeast growth assays, Cu (but not Fe or Mn) was identified as a substrate for NtZIP5B. Furthermore, GUS-based analysis showed that the tissue-specific activity of the NtZIP5B promoter was different in each of the Zn-/Cu-/Fe-/Mn deficiencies applied with/without Cd. The results indicate that NtZIP5B is involved in maintaining multi-metal homeostasis under conditions of Zn, Cu, Fe, and Mn deficiency, and also in the presence of Cd. It was concluded that the protein regulates the delivery of Zn and Cu specifically to targeted different root cells depending on the Zn/Cu/Fe/Mn status. Importantly, in the presence of Cd, the activity of the NtZIP5B promoter is lost in meristematic cells and increased in mature root cortex cells, which can be considered a manifestation of a defense mechanism against its toxic effects.

Metal Homeostasis in Land Plants: A Perpetual Balancing Act Beyond the Fulfilment of Metalloproteome Cofactor Demands

One of life's decisive innovations was to harness the catalytic power of metals for cellular chemistry. With life's expansion, global atmospheric and biogeochemical cycles underwent dramatic changes. Although initially harmful, they permitted the evolution of multicellularity and the colonization of land. In land plants as primary producers, metal homeostasis faces heightened demands, in part because soil is a challenging environment for nutrient balancing. To avoid both nutrient metal limitation and metal toxicity, plants must maintain the homeostasis of metals within tighter limits than the homeostasis of other minerals. This review describes the present model of protein metalation and sketches its transfer from unicellular organisms to land plants as complex multicellular organisms. The inseparable connection between metal and redox homeostasis increasingly draws our attention to more general regulatory roles of metals. Mineral co-option, the use of nutrient or other metals for functions other than nutrition, is an emerging concept beyond that of nutritional immunity.

Molecular Mechanisms of Plant Responses to Copper: From Deficiency to Excess

Copper (Cu) is an essential nutrient for plant growth and development. This metal serves as a constituent element or enzyme cofactor that participates in many biochemical pathways and plays a key role in photosynthesis, respiration, ethylene sensing, and antioxidant systems. The physiological significance of Cu uptake and compartmentalization in plants has been underestimated, despite the importance of Cu in cellular metabolic processes. As a micronutrient, Cu has low cellular requirements in plants. However, its bioavailability may be significantly reduced in alkaline or organic matter-rich soils. Cu deficiency is a severe and widespread nutritional disorder that affects plants. In contrast, excessive levels of available Cu in soil can inhibit plant photosynthesis and induce cellular oxidative stress. This can affect plant productivity and potentially pose serious health risks to humans via bioaccumulation in the food chain. Plants have evolved mechanisms to strictly regulate Cu uptake, transport, and cellular homeostasis during long-term environmental adaptation. This review provides a comprehensive overview of the diverse functions of Cu chelators, chaperones, and transporters involved in Cu homeostasis and their regulatory mechanisms in plant responses to varying Cu availability conditions. Finally, we identified that future research needs to enhance our understanding of the mechanisms regulating Cu deficiency or stress in plants. This will pave the way for improving the Cu utilization efficiency and/or Cu tolerance of crops grown in alkaline or Cu-contaminated soils.

The Uptake, Transfer, and Detoxification of Cadmium in Plants and Its Exogenous Effects

Cadmium (Cd) exerts a toxic influence on numerous crucial growth and development processes in plants, notably affecting seed germination rate, transpiration rate, chlorophyll content, and biomass. While considerable advances in Cd uptake and detoxification of plants have been made, the mechanisms by which plants adapt to and tolerate Cd toxicity remain elusive. This review focuses on the relationship between Cd and plants and the prospects for phytoremediation of Cd pollution. We highlight the following issues: (1) the present state of Cd pollution and its associated hazards, encompassing the sources and distribution of Cd and the risks posed to human health; (2) the mechanisms underlying the uptake and transport of Cd, including the physiological processes associated with the uptake, translocation, and detoxification of Cd, as well as the pertinent gene families implicated in these processes; (3) the detrimental effects of Cd on plants and the mechanisms of detoxification, such as the activation of resistance genes, root chelation, vacuolar compartmentalization, the activation of antioxidant systems and the generation of non-enzymatic antioxidants; (4) the practical application of phytoremediation and the impact of incorporating exogenous substances on the Cd tolerance of plants.

Exploration the interaction of cadmium and copper toxic effects in pakchoi (Brassica chinensis L) roots through combinatorial transcriptomic and weighted gene co-expression network analysis

The interaction between cadmium(Cd) and copper(Cu) during combined pollution can lead to more complex toxic effects on humans and plants.However, there is still a lack of sufficient understanding regarding the types of interactions at the plant molecular level and the response strategies of plants to combined pollution. To assess this, we investigated the phenotypic and transcriptomic patterns of pakchoi (Brassica chinensis L) roots in response to individual and combined pollution of Cd and Cu. The results showed that compared to single addition, the translocation factor of heavy metals in roots significantly decreased (p < 0.05) under the combined addition, resulting in higher accumulation of Cd and Cu in the roots. Transcriptomic analysis of pakchoi roots revealed that compared to single pollution, there were 312 and 1926 differentially expressed genes (DEGs) specifically regulated in the Cd2Cu20 and Cd2Cu100 combined treatments, respectively. By comparing the expression of these DEGs among different treatments, we found that the combined pollution of Cd and Cu mainly affected the transcriptome of the roots in an antagonistic manner. Enrichment analysis indicated that pakchoi roots upregulated the expression of genes involved in glucosetransferase activity, phospholipid homeostasis, proton transport, and the biosynthesis of phenylpropanoids and flavonoids to resist Cd and Cu combined pollution. Using weighted gene co-expression network analysis (WGCNA), we identified hub genes related to the accumulation of Cd and Cu in the roots, which mainly belonged to the LBD, thaumatin-like protein, ERF, MYB, WRKY, and TCP transcription factor families. This may reflect a transcription factor-driven trade-off strategy between heavy metal accumulation and growth in pakchoi roots. Additionally, compared to single metal pollution, the expression of genes related to Nramp, cation/H+ antiporters, and some belonging to the ABC transporter family in the pakchoi roots was significantly upregulated under combined pollution. This could lead to increased accumulation of Cd and Cu in the roots. These findings provide new insights into the interactions and toxic mechanisms of multiple metal combined pollution at the molecular level in plants.

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

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

Gene expression profiling of Jack Pine (Pinus banksiana) under copper stress: Identification of genes associated with copper resistance

Understanding the genetic response of plants to copper stress is a necessary step to improving the utility of plants for environmental remediation and restoration. The objectives of this study were to: 1) characterize the transcriptome of Jack Pine (Pinus banksiana) under copper stress, 2) analyze the gene expression profile shifts of genotypes exposed to copper ion toxicity, and 3) identify genes associated with copper resistance. Pinus banksiana seedlings were treated with 10 mmoles of copper and screened in a growth chamber. There were 6,213 upregulated and 29,038 downregulated genes expressed in the copper resistant genotypes compared to the susceptible genotypes at a high stringency based on the false discovery rate (FDR). Overall, 25,552 transcripts were assigned gene ontology. Among the top upregulated genes, the response to stress, the biosynthetic process, and the response to chemical stimuli terms represented the highest proportion of gene expression for the biological processes. For the molecular function category, the majority of expressed genes were associated with nucleotide binding followed by transporter activity, and kinase activity. The majority of upregulated genes were located in the plasma membrane while half of the total downregulated genes were associated with the extracellular region. Two candidate genes associated with copper resistance were identified including genes encoding for heavy metal-associated isoprenylated plant proteins (AtHIP20 and AtHIP26) and a gene encoding the pleiotropic drug resistance protein 1 (NtPDR1). This study represents the first report of transcriptomic responses of a conifer species to copper ions.

Identification and characterization of yellow stripe-like genes in maize suggest their roles in the uptake and transport of zinc and iron

BACKGROUND

Yellow Stripe-Like (YSL) proteins are involved in the uptake and transport of metal ions. They play important roles in maintaining the zinc and iron homeostasis in Arabidopsis, rice (Oryza sativa), and barley (Hordeum vulgare). However, proteins in this family have not been fully identified and comprehensively analyzed in maize (Zea mays L.).

RESULTS

In this study, we identified 19 ZmYSLs in the maize genome and analyzed their structural features. The results of a phylogenetic analysis showed that ZmYSLs are homologous to YSLs of Arabidopsis and rice, and these proteins are divided into four independent branches. Although their exons and introns have structural differences, the motif structure is relatively conserved. Analysis of the cis-regulatory elements in the promoters indicated that ZmYSLs might play a role in response to hypoxia and light. The results of RNA sequencing and quantitative real-time PCR analysis revealed that ZmYSLs are expressed in various tissues and respond differently to zinc and iron deficiency. The subcellular localization of ZmYSLs in the protoplast of maize mesophyll cells showed that they may function in the membrane system.

CONCLUSIONS

This study provided important information for the further functional analysis of ZmYSL, especially in the spatio-temporal expression and adaptation to nutrient deficiency stress. Our findings provided important genes resources for the maize biofortification.

Zinc accumulation in Atriplex lentiformis is driven by plant genes and the soil microbiome

Successful phytoremediation of acidic metal-contaminated mine tailings requires amendments to condition tailings properties prior to plant establishment. This conditioning process is complex and includes multiple changes in tailings bio-physico-chemical properties. The objective of this project is to identify relationships between tailings properties, the soil microbiome, and plant stress response genes during growth of Atriplex lentiformis in compost-amended (10 %, 15 %, 20 % w/w) mine tailings. Analyses include RNA-Seq for plant root gene expression, 16S rRNA amplicon sequencing for bacterial/archaeal communities, metal concentrations in both tailings and plant organs, and phenotypic measures of plant stress. Zn accumulation in A. lentiformis leaves varied with compost levels and was the highest in the intermediate treatment (15 %, TC15). Microbial analysis identified Alicyclobacillus, Hydrotalea, and Pseudolabrys taxa with the highest relative abundance in TC15, and these taxa were strongly associated with Zn accumulation. Furthermore, we identified 190 root genes with significant gene expression changes. These root genes were associated with different pathways including, abscisic acid and auxin signaling, defense responses, ion channels, metal ion binding, oxidative stress, transcription regulation, and transmembrane transport. However, root gene expression changes were not driven by the increasing levels of compost. For example, there were 15 genes that were up-regulated in TC15, whereas 106 genes were down-regulated in TC15. The variables analyzed explained 86 % of the variance in Zn accumulation in A. lentiformis leaves. Importantly, Zn accumulation was driven by Zn shoot concentrations, leaf stress symptoms, plant root genes, and microbial taxa. Therefore, our results suggest there are strong plant-microbiome associations that drive Zn accumulation in A. lentiformis and different plant gene pathways are involved in alleviating varying levels of metal stress. Future work is needed to gain a mechanistic understanding of these plant-microbiome interactions to optimize phytoremediation strategies as they will govern the success or failure of the revegetation process.

Black sheep, dark horses, and colorful dogs: a review on the current state of the Gene Ontology with respect to iron homeostasis in Arabidopsis thaliana

Cellular homeostasis of the micronutrient iron is highly regulated in plants and responsive to nutrition, stress, and developmental signals. Genes for iron management encode metal and other transporters, enzymes synthesizing chelators and reducing substances, transcription factors, and several types of regulators. In transcriptome or proteome datasets, such iron homeostasis-related genes are frequently found to be differentially regulated. A common method to detect whether a specific cellular pathway is affected in the transcriptome data set is to perform Gene Ontology (GO) enrichment analysis. Hence, the GO database is a widely used resource for annotating genes and identifying enriched biological pathways in Arabidopsis thaliana. However, iron homeostasis-related GO terms do not consistently reflect gene associations and levels of evidence in iron homeostasis. Some genes in the existing iron homeostasis GO terms lack direct evidence of involvement in iron homeostasis. In other aspects, the existing GO terms for iron homeostasis are incomplete and do not reflect the known biological functions associated with iron homeostasis. This can lead to potential errors in the automatic annotation and interpretation of GO term enrichment analyses. We suggest that applicable evidence codes be used to add missing genes and their respective ortholog/paralog groups to make the iron homeostasis-related GO terms more complete and reliable. There is a high likelihood of finding new iron homeostasis-relevant members in gene groups and families like the ZIP, ZIF, ZIFL, MTP, OPT, MATE, ABCG, PDR, HMA, and HMP. Hence, we compiled comprehensive lists of genes involved in iron homeostasis that can be used for custom enrichment analysis in transcriptomic or proteomic studies, including genes with direct experimental evidence, those regulated by central transcription factors, and missing members of small gene families or ortholog/paralog groups. As we provide gene annotation and literature alongside, the gene lists can serve multiple computational approaches. In summary, these gene lists provide a valuable resource for researchers studying iron homeostasis in A. thaliana, while they also emphasize the importance of improving the accuracy and comprehensiveness of the Gene Ontology.

Transcriptional response of Cu-deficient barley (Hordeum vulgare L.) to foliar-applied nano-Cu: Molecular crosstalk between Cu loading into plants and changes in Cu homeostasis genes

For safe and effective nutrient management, the cutting-edge approaches to plant fertilization are continuously developed. The aim of the study was to analyze the transcriptional response of barley suffering from Cu deficiency to foliar application of nanoparticulate Cu (nano-Cu) and its ionic form (CuSO4) at 100 and 1000 mg L-1 for the examination of their supplementing effect. The initial interactions of Cu-compounds with barley leaves were analyzed with spectroscopic (ICP-OES) and microscopic (SEM-EDS) methods. To determine Cu cellular status, the impact of Cu-compounds on the expression of genes involved in regulating Cu homeostasis (PAA1, PAA2, RAN1, COPT5), aquaporins (NIP2.1, PIP1.1, TIP1.1, TIP1.2) and antioxidant defense response (SOD CuZn, SOD Fe, SOD Mn, CAT) after 1 and 7 days of exposure was analyzed. Although Cu accumulation in plant leaves was detected overtime, the Cu content in leaves exposed to nano-Cu for 7 days was 44.5% lower than in CuSO4 at 100 mg L-1. However, nano-Cu aggregates remaining on the leaf surface indicated a potential difference between measured Cu content and the real Cu pool present in the plant. Our study revealed significant changes in the pattern of gene expression overtime depending on Cu-compound type and dose. Despite the initial puzzling patterns of gene expression, after 7 days all Cu transporters showed significant down-regulation under Cu-compounds exposure to prevent Cu excess in plant cells. Conversely, aquaporin gene expression was induced after 7 days, especially by nano-Cu and CuSO4 at 100 mg L-1 due to the stimulatory effect of low Cu doses. Our study revealed that the gradual release of Cu ions from nano-Cu at a lower rate provided a milder molecular response than CuSO4. It might indicate that nano-Cu maintained better metal balance in plants than the conventional compounds, thus may be considered as a long-term supplier of Cu.

Nicotianamine: A Key Player in Metal Homeostasis and Hyperaccumulation in Plants

Nicotianamine (NA) is a low-molecular-weight N-containing metal-binding ligand, whose accumulation in plant organs changes under metal deficiency or excess. Although NA biosynthesis can be induced in vivo by various metals, this non-proteinogenic amino acid is mainly involved in the detoxification and transport of iron, zinc, nickel, copper and manganese. This review summarizes the current knowledge on NA biosynthesis and its regulation, considers the mechanisms of NA secretion by plant roots, as well as the mechanisms of intracellular transport of NA and its complexes with metals, and its role in radial and long-distance metal transport. Its role in metal tolerance is also discussed. The NA contents in excluders, storing metals primarily in roots, and in hyperaccumulators, accumulating metals mainly in shoots, are compared. The available data suggest that NA plays an important role in maintaining metal homeostasis and hyperaccumulation mechanisms. The study of metal-binding compounds is of interdisciplinary significance, not only regarding their effects on metal toxicity in plants, but also in connection with the development of biofortification approaches to increase the metal contents, primarily of iron and zinc, in agricultural plants, since the deficiency of these elements in food crops seriously affects human health.

Transcriptomic Changes Induced by Low and High Concentrations of Heavy Metal Exposure in Ulva pertusa

The impact of sewage and wastewater pollution on marine ecosystems is of increasing concern due to the rapid accumulation of heavy metals in seaweeds inhabiting near-shore environments. Seaweeds can be severely damaged by heavy metals throughout their life cycles. Although the physiological and ecological effects of heavy metal exposure have been studied, there is limited research on their molecular responses. Ulva pertusa is a prevalent seaweed species in South Korea and is ecologically significant in coastal ecosystems. We utilized high-throughput RNA sequencing to analyze changes in the transcriptome profiles of U. pertusa under low concentrations of heavy metals (MPS) and high concentrations of copper (MPS-Cu) and cadmium (MPS-Cd). Differential gene expression analysis revealed that 53 (control vs. MPS), 27 (MPS vs. MPS-Cd), and 725 (MPS vs. MPS-Cu) genes were expressed differentially. Differentially expressed genes identified in our study included those with protective roles against oxidative stress and those involved in metal transport to the vacuole. Furthermore, exposure to heavy metal stress had a negative impact on the photosynthetic apparatus structural proteins of U. pertusa, resulting in photosynthetic inhibition. Moreover, exposure to high concentrations of copper resulted in the activation of carbon-related metabolism. These findings contribute to our understanding of the molecular mechanisms underlying heavy metal toxicity in U. pertusa.

Diversity and expression analysis of ZIP transporters and associated metabolites under zinc and iron stress in Capsicum

The members of ZRT, IRT-like protein (ZIP) family are involved in the uptake and transportation of several metal ions. Here, we report a comprehensive identification of ZIP transporter genes from Capsicum annuum, C. chinense, and C. baccatum, and their expression analysis under Zn and Fe stress. Changes in root morphology and differential accumulation of several metabolites from sugars, amino acids, carboxylic acids, and fatty acids in root and leaf tissues of plants in the absence of Zn and Fe were observed. Further, metabolites such as L-aspartic acid, 2-ketoglutaric acids, β-L-fucopyranose, quininic acid, chlorogenic acid, and aucubin were significantly upregulated in root and leaf tissues under Zn/Fe deprived conditions. qRT-PCR analysis of 17 CaZIPs in different tissues revealed tissue-specific expression of CaZIP1-2, CaZIP4-8, CaZIP13, and CaZIP16-17 under normal conditions. However, the absence of Zn and Fe significantly induced the expression of CaZIP4-5, CaZIP7-9, and CaZIP14 genes in root and leaf tissues. Additionally, in the absence of Fe, upregulation of CaZIP4-5 and CaZIP8 and increased uptake of mineral elements Cu, Zn, Mg, P, and S were observed in roots, suggesting their potential role in metal-ion uptake in Capsicum. The identified genes provide the basis for future studies of mineral uptake and their biofortification to increase the nutritional values in Capsicum.

Zinc/iron-regulated transporter-like protein gene family in Theobroma cacao L: Characteristics, evolution, function and 3D structure analysis

The zinc/iron-regulated transporter-like protein (ZIP) gene family first identified in plants is highly distributed in the plant kingdom. This family has previously been reported to transport several essential and non-essential cationic elements, including those toxic to many economically important crops such as cacao (Theobroma cacao L.). In this article, we present a detailed study on physicochemical properties, evolution, duplication, gene structure, promoter region and TcZIP family three-dimensional protein structure. A total of 11 TcZIP genes have been identified to encode proteins from 309 to 435 aa, with localization in the plasma membrane and chloroplast, containing 6-9 putative domains (TM). Interspecies phylogenetic analysis subdivided the ZIP proteins into four groups. Segmental duplication events significantly contributed to the expansion of TcZIP genes. These genes underwent high pressure of purifying selection. The three-dimensional structure of the proteins showed that α helix conformations are predominant with several pocket sites, containing the metal binding site, with the residues leucine (LEU), alanine (ALA), glycine (GLY), serine (SER), lysine (LYS) and histidine (HIS) the most predicted. Regarding the analysis of the protein-protein interaction and enrichment of the gene ontology, four biological processes were assigned, the most important being the cation transport. These new discoveries expand the knowledge about the function, evolution, protein structures and interaction of ZIP family proteins in cacao and contribute to develop cacao genotypes enriched with important mineral nutrients as well as genotypes that bioaccumulate or exclude toxic metals.

Silicon in action: Between iron scarcity and excess copper

Essential micronutrients belonging to the transition metals, such as Fe and Cu, are indispensable for plant growth and stress tolerance; however, when present in excess, they can become potentially dangerous producers of reactive oxygen species. Therefore, their homeostases must be strictly regulated. Both microelement deficiencies and elevated concentrations of heavy metals in the soil are global problems that reduce the nutritional value of crops and seriously affect human health. Silicon, a beneficial element known for its protective properties, has been reported to alleviate the symptoms of Cu toxicity and Fe deficiency stress in plants; however, we are still far from a comprehensive understanding of the underlying molecular mechanisms. Although Si-mediated mitigation of these stresses has been clearly demonstrated for some species, the effects of Si vary depending on plant species, growing conditions and experimental design. In this review, the proposed mechanistic models explaining the effect of Si are summarized and discussed. Iron and copper compete for the common metal transporters and share the same transport routes, hence, inadequate concentration of one element leads to disturbances of another. Silicon is reported to beneficially influence not only the distribution of the element supplied below or above the optimal concentration, but also the distribution of other microelements, as well as their molar ratios. The influence of Si on Cu immobilization and retention in the root, as well as Si-induced Fe remobilization from the source to the sink organs are of vital importance. The changes in cellular Cu and Fe localization are considered to play a crucial role in restoring homeostasis of these microelements. Silicon has been shown to stimulate the accumulation of metal chelators involved in both the mobilization of deficient elements and scavenging excess heavy metals. Research into the mechanisms of the ameliorative effects of Si is valuable for reducing mineral stress in plants and improving the nutritional value of crops. This review aims to provide a thorough and critical overview of the current state of knowledge in this field and to discuss discrepancies in the observed effects of Si and different views on its mode of action.

Comparative Transcriptome Analysis Reveals Complex Physiological Response and Gene Regulation in Peanut Roots and Leaves under Manganese Toxicity Stress

Excess Manganese (Mn) is toxic to plants and reduces crop production. Although physiological and molecular pathways may drive plant responses to Mn toxicity, few studies have evaluated Mn tolerance capacity in roots and leaves. As a result, the processes behind Mn tolerance in various plant tissue or organ are unclear. The reactivity of peanut (Arachis hypogaea) to Mn toxicity stress was examined in this study. Mn oxidation spots developed on peanut leaves, and the root growth was inhibited under Mn toxicity stress. The physiological results revealed that under Mn toxicity stress, the activities of antioxidases and the content of proline in roots and leaves were greatly elevated, whereas the content of soluble protein decreased. In addition, manganese and iron ion content in roots and leaves increased significantly, but magnesium ion content decreased drastically. The differentially expressed genes (DEGs) in peanut roots and leaves in response to Mn toxicity were subsequently identified using genome-wide transcriptome analysis. Transcriptomic profiling results showed that 731 and 4589 DEGs were discovered individually in roots and leaves, respectively. Furthermore, only 310 DEGs were frequently adjusted and controlled in peanut roots and leaves, indicating peanut roots and leaves exhibited various toxicity responses to Mn. The results of qRT-PCR suggested that the gene expression of many DEGs in roots and leaves was inconsistent, indicating a more complex regulation of DEGs. Therefore, different regulatory mechanisms are present in peanut roots and leaves in response to Mn toxicity stress. The findings of this study can serve as a starting point for further research into the molecular mechanism of important functional genes in peanut roots and leaves that regulate peanut tolerance to Mn poisoning.

Physiology and proteomics reveal Fulvic acid mitigates Cadmium adverse effects on growth and photosynthetic properties of lettuce

Understanding the molecular mechanisms of plants in response to Cd stress is crucial for improving plants adaptation to Cd stress. Fulvic acid (FA) is an active humic substance that is often used as a soil conditioner. However, there are few reports on the role of FA against Cd stress. The aim of this study was to determine the effects of Fulvic acid on alleviation of Cd toxicity in lettuce (Lactuca sativa L) under hydroponic conditions. Our results showed that 20 μmol/L Cd stress significantly reduced photosynthetic pigment metabolism and the expression of photosynthetic apparatus-related proteins, thereby inhibiting photosynthetic electron transport, net photosynthetic rate and negatively affecting photosynthetic carbon assimilation and growth of lettuce. However, proteomic findings suggest that the application of FA can reduce the adverse effects of Cd contamination. Compared to Cd stress alone, FA significantly increased the expression of Light-harvesting proteins, reaction center and electron transport-related proteins. Further results showed that FA at 0.5 g/L reduced the uptake of Cd by the roots, resulting in a 23.5% reduction in total Cd content in lettuce. Moreover, FA enhanced S metabolism and rebuilt redox homeostasis in cells. Overall, these findings provide new insights into the mechanism of cadmium toxicity mitigation in lettuce by FA. Which is recommended as an eco-friendly tool for improving the photosynthesis performance and biomass of lettuce under Cd stress.

Genome-wide identification of the ZIP gene family in lettuce (Lactuca sativa L.) and expression analysis under different element stress

The ZIP protein (ZRT, the IRT-like protein) is an important metal transporter that transports Zn, Fe, and other divalent metal ions in plants. In this study, we identified 20 ZIP genes in lettuce (Lactuca sativa L.). We used bioinformatics methods and renamed them according to their E value in hmmsearch. We also analyzed their gene structure, chromosomal location, constructed a phylogenetic tree, conserved motifs, performed synonymous analysis and responses to abiotic stresses. The results show that these LsZIP genes have 3-11 exons and were distributed unequally on 8 of the 9 chromosomes in lettuce. Based on phylogenetic analyses, the LsZIP gene family can be divided into three subfamilies, and the LsZIP genes within the same subfamily shared similar gene structure. The LsZIP genes contain 12 Motifs, of which Motif1 to Motif8 are widely distributed in group Ⅰ. Furthermore, the LsZIP gene contains numerous hormones and anti-stress response elements. Real-time quantitative PCR demonstrated that most LsZIP genes is up-regulated under the elemental stress in this experiment, indicating that they are positively regulated. But different elemental stressors can induce the expression of LsZIP gene to varying degrees. The LsZIP genes also change in response to different elemental stresses. The present study serves as a basic foundation for future functional studies on the lettuce ZIP family.

Functional Characterization of MaZIP4, a Gene Regulating Copper Stress Tolerance in Mulberry (Morus atropurpurea R.)

ZIP4 (zinc transporter 4) plays important roles in transporting Cu²⁺ ions in plants, which may contribute to the maintenance of plant metal homeostasis in growth, plant development and normal physiological metabolism. However, ZIP4 transporters have not been described in mulberry and the exact function of ZIP4 transporters in regulating the homeostasis of Cu in mulberry remains unclear. In this study, a new ZIP4 gene (MaZIP4) was isolated and cloned from Morus atropurpurea R. Phylogenetic analysis of amino sequences suggested that the amino-acid sequence of the MaZIP4 protein shows high homology with other ZIP4 proteins of Morus notabilis, Trema orientale, Ziziphus jujube and Cannabis sativa. In addition, a MaZIP4 silenced line was successfully constructed using virus-induced gene silencing (VIGS). The analysis of MaZIP4 expression by quantitative real-time PCR in mulberry showed that the level of MaZIP4 expression increased with increasing Cu concentration until the Cu concentration reached 800 ppm. Relative to the blank (WT) and the negative controls, malondialdehyde (MDA) levels increased significantly and rose with increasing Cu concentration in the MaZIP4 silenced line, whereas the soluble protein and proline content, superoxide dismutase (SOD) and peroxidase (POD) activities of these transgenic plants were lower. These results indicated that MaZIP4 may play an important role in the resistance of mulberry to Cu stress.

The Role of Sulfur in Agronomic Biofortification with Essential Micronutrients

Sulfur (S) is an essential macronutrient for plants, being necessary for their growth and metabolism and exhibiting diverse roles throughout their life cycles. Inside the plant body, S is present either in one of its inorganic forms or incorporated in an organic compound. Moreover, organic S compounds may contain S in its reduced or oxidized form. Among others, S plays roles in maintaining the homeostasis of essential micronutrients, e.g., iron (Fe), copper (Cu), zinc (Zn), and manganese (Mn). One of the most well-known connections is homeostasis between S and Fe, mainly in terms of the role of S in uptake, transportation, and distribution of Fe, as well as the functional interactions of S with Fe in the Fe-S clusters. This review reports the available information describing the connections between the homeostasis of S and Fe, Cu, Zn, and Mn in plants. The roles of S- or sulfur-derived organic ligands in metal uptake and translocation within the plant are highlighted. Moreover, the roles of these micronutrients in S homeostasis are also discussed.

The key micronutrient copper orchestrates broad-spectrum virus resistance in rice

Copper is a critical regulator of plant growth and development. However, the mechanisms by which copper responds to virus invasion are unclear. We previously showed that SPL9-mediated transcriptional activation of miR528 adds a previously unidentified regulatory layer to the established ARGONAUTE (AGO18)-miR528-L-ascorbate oxidase (AO) antiviral defense. Here, we report that rice promotes copper accumulation in shoots by inducing copper transporter genes, including HMA5 and COPT, to counteract viral infection. Copper suppresses the transcriptional activation of miR528 by inhibiting the protein level of SPL9, thus alleviating miR528-mediated cleavage of AO transcripts to strengthen the antiviral response. Loss-of-function mutations in HMA5, COPT1, and COPT5 caused a significant reduction in copper accumulation and plant viral resistance because of the increased SPL9-mediated miR528 transcription. Gain in viral susceptibility was mitigated when SPL9 was mutated in the hma5 mutant background. Our study elucidates the molecular mechanisms and regulatory networks of copper homeostasis and the SPL9-miR528-AO antiviral pathway.

Insights to improve the plant nutrient transport by CRISPR/Cas system

We need to improve food production to feed the ever growing world population especially in a changing climate. Nutrient deficiency in soils is one of the primary bottlenecks affecting the crop production both in developed and developing countries. Farmers are forced to apply synthetic fertilizers to improve the crop production to meet the demand. Understanding the mechanism of nutrient transport is helpful to improve the nutrient-use efficiency of crops and promote the sustainable agriculture. Many transporters involved in the acquisition, export and redistribution of nutrients in plants are characterized. In these studies, heterologous systems like yeast and Xenopus were most frequently used to study the transport function of plant nutrient transporters. CRIPSR/Cas system introduced recently has taken central stage for efficient genome editing in diverse organisms including plants. In this review, we discuss the key nutrient transporters involved in the acquisition and redistribution of nutrients from soil. We draw insights on the possible application CRISPR/Cas system for improving the nutrient transport in plants by engineering key residues of nutrient transporters, transcriptional regulation of nutrient transport signals, engineering motifs in promoters and transcription factors. CRISPR-based engineering of plant nutrient transport not only helps to study the process in native plants with conserved regulatory system but also aid to develop non-transgenic crops with better nutrient use-efficiency. This will reduce the application of synthetic fertilizers and promote the sustainable agriculture strengthening the food and nutrient security.

Zinc deficiency responses: bridging the gap between Arabidopsis and dicotyledonous crops

Zinc (Zn) deficiency is a widespread phenomenon in agricultural soils worldwide and has a major impact on crop yield and quality, and hence on human nutrition and health. Although dicotyledonous crops represent >30% of human plant-based nutrition, relatively few efforts have been dedicated to the investigation of Zn deficiency response mechanisms in dicotyledonous, in contrast to monocotyledonous crops, such as rice or barley. Here, we describe the Zn requirement and impact of Zn deficiency in several economically important dicotyledonous crops, Phaseolus vulgaris, Glycine max, Brassica oleracea, and Solanum lycopersicum. We briefly review our current knowledge of the Zn deficiency response in Arabidopsis and outline how this knowledge is translated in dicotyledonous crops. We highlight commonalities and differences between dicotyledonous species (and with monocotyledonous species) regarding the function and regulation of Zn transporters and chelators, as well as the Zn-sensing mechanisms and the role of hormones in the Zn deficiency response. Moreover, we show how the Zn homeostatic network intimately interacts with other nutrients, such as iron or phosphate. Finally, we outline how variation in Zn deficiency tolerance and Zn use efficiency among cultivars of dicotyledonous species can be leveraged for the design of Zn biofortification strategies.

High-value pleiotropic genes for developing multiple stress-tolerant biofortified crops for 21st-century challenges

The agriculture-based livelihood systems that are already vulnerable due to multiple challenges face immediate risk of increased crop failures due to weather vagaries. As breeders and biotechnologists, our strategy is to advance and innovate breeding for weather-proofing crops. Plant stress tolerance is a genetically complex trait. Additionally, crops rarely face a single type of stress in isolation, and it is difficult for plants to deal with multiple stresses simultaneously. One of the most helpful approaches to creating stress-resilient crops is genome editing and trans- or cis-genesis. Out of hundreds of stress-responsive genes, many have been used to impart tolerance against a particular stress factor, while a few used in combination for gene pyramiding against multiple stresses. However, a better approach would be to use multi-role pleiotropic genes that enable plants to adapt to numerous environmental stresses simultaneously. Herein we attempt to integrate and present the scattered information published in the past three decades about these pleiotropic genes for crop improvement and remodeling future cropping systems. Research articles validating functional roles of genes in transgenic plants were used to create groups of multi-role pleiotropic genes that could be candidate genes for developing weather-proof crop varieties. These biotech crop varieties will help create 'high-value farms' to meet the goal of a sustainable increase in global food productivity and stabilize food prices by ensuring a fluctuation-free assured food supply. It could also help create a gene repository through artificial gene synthesis for 'resilient high-value food production' for the 21st century.

Changeable effects of coexisting heavy metals on transfer of cadmium from soils to wheat grains

Cadmium (Cd) and other heavy metals usually coexist in soils. Effects of coexisting heavy metals on the accumulation and transfer of Cd in field soils by wheat remain poorly understood. Here we revealed changeable effects of coexisting Pb, Zn and Cu on the Cd transfer from soils to wheat grains. Soil burdens of Cd were found to exhibit positive correlations (r = 0.459-0.946) with those of coexisting Pb, Zn and Cu (particularly Pb). Effects of three coexisting metals on to the uptake of Cd by wheat varied in the directions and/or extents with types of metals and transfer processes of Cd. Coexisting Zn inhibited the uptake of Cd by wheat grains to higher extent than Pb and Cu. Soil Zn, along with soil Cd, soil pH and soil Ca, was used to construct the predictive model of grain Cd (R² = 0.868). External verifications of the model on 572 datasets of large representation performed well. The predictive accuracy was about 54%, 73% and 89% for a factor of 1, 2 and 5 above and below the ideal fit, respectively. This finding has practical interest in risk assessments and remediation measures of Cd-contaminated soil sites in regional scales.

Root-to-shoot iron partitioning in Arabidopsis requires IRON-REGULATED TRANSPORTER1 (IRT1) protein but not its iron(II) transport function

IRON-REGULATED TRANSPORTER1 (IRT1) is the root high-affinity ferrous iron (Fe) uptake system and indispensable for the completion of the life cycle of Arabidopsis thaliana without vigorous Fe supplementation. Here we provide evidence supporting a second role of IRT1 in root-to-shoot partitioning of Fe. We show that irt1 mutants overaccumulate Fe in roots, most prominently in the cortex of the differentiation zone in irt1-2, compared to the wild type. Shoots of irt1-2 are severely Fe-deficient according to Fe content and marker transcripts, as expected. We generated irt1-2 lines producing IRT1 mutant variants carrying single amino-acid substitutions of key residues in transmembrane helices IV and V, Ser206 and His232, which are required for transport activity in yeast. Root short-term ⁵⁵ Fe uptake rates were uninformative concerning IRT1-mediated transport. Overall irt1-like concentrations of the secondary substrate Mn suggested that the transgenic Arabidopsis lines also remain incapable of IRT1-mediated root Fe uptake. Yet, IRT1_S206A partially complements rosette dwarfing and leaf chlorosis of irt1-2, as well as root-to-shoot Fe partitioning and gene expression defects of irt1-2, all of which are fully complemented by wild-type IRT1. Taken together, these results suggest a regulatory function for IRT1 in root-to-shoot Fe partitioning that does not require Fe transport activity of IRT1. Among the genes of which transcript levels are partially dependent on IRT1, we identify MYB DOMAIN PROTEIN10, MYB DOMAIN PROTEIN72 and NICOTIANAMINE SYNTHASE4 as candidates for effecting IRT1-dependent Fe mobilization in roots. Understanding the biological functions of IRT1 will help to improve Fe nutrition and the nutritional quality of agricultural crops.

Metal tolerance in plants: Molecular and physicochemical interface determines the "not so heavy effect" of heavy metals

An increase in technological interventions and ruthless urbanization in the name of development has deteriorated our environment over time and caused the buildup of heavy metals (HMs) in the soil and water resources. These heavy metals are gaining increased access into our food chain through the plant and/or animal-based products, to adversely impact human health. The issue of how to restrict the entry of HMs or modulate their response in event of their ingress into the plant system is worrisome. The current knowledge on the interactive-regulatory role and contribution of different physical, biophysical, biochemical, physiological, and molecular factors that determine the heavy metal availability-uptake-partitioning dynamics in the soil-plant-environment needs to be updated. The present review critically analyses the interactive overlaps between different adaptation and tolerance strategies that may be causally related to their cellular localization, conjugation and homeostasis, a relative affinity for the transporters, rhizosphere modifications, activation of efflux pumps and vacuolar sequestration that singly or collectively determine a plant's response to HM stress. Recently postulated role of gaseous pollutants such as SO₂ and other secondary metabolites in heavy metal tolerance, which may be regulated at the whole plant and/or tissue/cell is discussed to delineate and work towards a "not so heavy" response of plants to heavy metals present in the contaminated soils.

Low-molecular-weight ligands in plants: role in metal homeostasis and hyperaccumulation

Mineral nutrition is one of the key factors determining plant productivity. In plants, metal homeostasis is achieved through the functioning of a complex system governing metal uptake, translocation, distribution, and sequestration, leading to the maintenance of a regulated delivery of micronutrients to metal-requiring processes as well as detoxification of excess or non-essential metals. Low-molecular-weight ligands, such as nicotianamine, histidine, phytochelatins, phytosiderophores, and organic acids, play an important role in metal transport and detoxification in plants. Nicotianamine and histidine are also involved in metal hyperaccumulation, which determines the ability of some plant species to accumulate a large amount of metals in their shoots. In this review we extensively summarize and discuss the current knowledge of the main pathways for the biosynthesis of these ligands, their involvement in metal uptake, radial and long-distance transport, as well as metal influx, isolation and sequestration in plant tissues and cell compartments. It is analyzed how diverse endogenous ligand levels in plants can determine their different tolerance to metal toxic effects. This review focuses on recent advances in understanding the physiological role of these compounds in metal homeostasis, which is an essential task of modern ionomics and plant physiology. It is of key importance in studying the influence of metal deficiency or excess on various physiological processes, which is a prerequisite to the improvement of micronutrient uptake efficiency and crop productivity and to the development of a variety of applications in phytoremediation, phytomining, biofortification, and nutritional crop safety.

Zinc uptake and HMA4 activity are required for micro- and macroelement balance in tobacco (Nicotiana tabacum)

The pleiotropic effects of zinc deficiency on ion homeostasis have already been described in several plants. Tobacco (Nicotiana tabacum) heavy metal ATPases HMA4.1 and HMA4.2 are involved in zinc and cadmium root-to-shoot translocation. In previous research, we have shown that N. tabacum HMA4 RNAi plants and HMA4 double-nonsense mutants exhibit strongly reduced zinc and cadmium levels in leaves as well as stunted growth. In this study, the ionome and transcriptome of these lines were investigated to better characterize the effect of reduced zinc levels and to understand the impaired growth phenotype. We found that, under standard greenhouse fertilization rates, these lines accumulated up to 4- to 6-fold more phosphorus, iron, manganese, and copper than their respective controls. Under field conditions, HMA4 double-mutant plants also exhibited similar accumulation phenotypes, albeit to a lower extent. In both HMA4 RNAi plants and HMA4 mutants, transcription analysis showed a local zinc-deficiency response in leaves as well as an FIT1-mediated iron-deficiency response in roots, likely contributing to iron and manganese uptake at the root level. A phosphate-starvation response involving HHO2 was also observed in HMA4-impaired plant leaves. The high level of phosphorus observed in HMA4-impaired plants is correlated with leaf swelling and necrosis. The upregulation of aquaporin genes is in line with cellular water influx and the observed leaf swelling phenotype. These results highlight the involvement of HMA4 in zinc homeostasis and related regulatory processes that balance the micro- and macroelements in above-ground organs.

Transcriptome Profiling of Cu Stressed Petunia Petals Reveals Candidate Genes Involved in Fe and Cu Crosstalk

Copper (Cu) is an essential element for most living plants, but it is toxic for plants when present in excess. To better understand the response mechanism under excess Cu in plants, especially in flowers, transcriptome sequencing on petunia buds and opened flowers under excess Cu was performed. Interestingly, the transcript level of FIT-independent Fe deficiency response genes was significantly affected in Cu stressed petals, probably regulated by basic-helix-loop-helix 121 (bHLH121), while no difference was found in Fe content. Notably, the expression level of bHLH121 was significantly down-regulated in petals under excess Cu. In addition, the expression level of genes related to photosystem II (PSII), photosystem I (PSI), cytochrome b₆/f complex, the light-harvesting chlorophyll II complex and electron carriers showed disordered expression profiles in petals under excess Cu, thus photosynthesis parameters, including the maximum PSII efficiency (F_V/F_M), nonphotochemical quenching (NPQ), quantum yield of the PSII (ΦPS(II)) and photochemical quenching coefficient (qP), were reduced in Cu stressed petals. Moreover, the chlorophyll a content was significantly reduced, while the chlorophyll b content was not affected, probably caused by the increased expression of chlorophyllide a oxygenase (CAO). Together, we provide new insight into excess Cu response and the Cu–Fe crosstalk in flowers.

Phosphorus Starvation- and Zinc Excess-Induced Astragalus sinicus AsZIP2 Zinc Transporter Is Suppressed by Arbuscular Mycorrhizal Symbiosis

Zinc (Zn) is one of the most essential micronutrients for plant growth and metabolism, but Zn excess can impair many basic metabolic processes in plant cells. In agriculture, crops often experience low phosphate (Pi) and high Zn double nutrient stresses because of inordinate agro-industrial activities, while the dual benefit of arbuscular mycorrhizal (AM) fungi protects plants from experiencing both deficient and toxic nutrient stresses. Although crosstalk between Pi and Zn nutrients in plants have been extensively studied at the physiological level, the molecular basis of how Pi starvation triggers Zn over-accumulation in plants and how AM plants coordinately modulate the Pi and Zn nutrient homeostasis remains to be elucidated. Here, we report that a novel AsZIP2 gene, a Chinese milk vetch (Astragalus sinicus) member of the ZIP gene family, participates in the interaction between Pi and Zn nutrient homeostasis in plants. Phylogenetic analysis revealed that this AsZIP2 protein was closely related to the orthologous Medicago MtZIP2 and Arabidopsis AtZIP2 transporters. Gene expression analysis indicated that AsZIP2 was highly induced in roots by Pi starvation or Zn excess yet attenuated by arbuscular mycorrhization in a Pi-dependent manner. Subcellular localization and heterologous expression experiments further showed that AsZIP2 encoded a functional plasma membrane-localized transporter that mediated Zn uptake in yeast. Moreover, overexpression of AsZIP2 in A. sinicus resulted in the over-accumulation of Zn concentration in roots at low Pi or excessive Zn concentrations, whereas AsZIP2 silencing lines displayed an even more reduced Zn concentration than control lines under such conditions. Our results reveal that the AsZIP2 transporter functioned in Zn over-accumulation in roots during Pi starvation or high Zn supply but was repressed by AM symbiosis in a Pi-dependent manner. These findings also provide new insights into the AsZIP2 gene acting in the regulation of Zn homeostasis in mycorrhizal plants through Pi signal.

Potential Use of Copper-Contaminated Soils for Hemp (Cannabis sativa L.) Cultivation

To mitigate climate change, reducing greenhouse gas emissions can be achieved by decreasing the use of fossil fuels and increasing that of alternative sources, such as energy crops. However, one of the most important problems in the use of biomass as a fuel is that of changing soil use and consumption, leading to competition with food crops. We addressed the topic by evaluating the possibility to exploit contaminated areas for energy crops cultivation. Indeed, soil contamination makes land inappropriate for cultivation, with damaging consequences for ecosystems, as well as posing serious health hazards to living beings. Specifically, this work aimed to evaluate the ability of hemp (Cannabis sativa L.) plants to grow on a copper (Cu)-contaminated medium. In addition, the effectiveness of an environment-friendly treatment with sulfate in improving plant ability to cope with Cu-induced oxidative stress was also explored. Results showed that plants were able to grow at high Cu concentrations. Therefore, hemp could represent an interesting energy crop in Cu-contaminated soils. Although the response of Cu-treated plants was evidenced by the increase in thiol content, following modulation of sulfur metabolism, it remains to be clarified whether the use of exogenous sulfate could be an agronomic practice to improve crop performance under these edaphic conditions.

Malus rootstocks affect copper accumulation and tolerance in trees by regulating copper mobility, physiological responses, and gene expression patterns

We investigated the roles of rootstocks in Cu accumulation and tolerance in Malus plants by grafting 'Hanfu' (HF) scions onto M. baccata (Mb) and M. prunifolia (Mp) rootstocks, which have different Cu tolerances. The grafts were exposed to basal or excess Cu for 20 d. Excess Cu-treated HF/Mb had less biomass, and pronounced root architecture deformation and leaf ultrastructure damage than excess Cu-challenged HF/Mp. Root Cu concentrations and bio-concentration factor (BCF) were higher in HF/Mp than HF/Mb, whereas HF/Mb had higher stem and leaf Cu concentrations than HF/Mp. Excess Cu lowered root and aerial tissue BCF and translocation factor (T_f) in all plants; however, T_f was markedly higher in HF/Mb than in HF/Mp. The subcellular distribution of Cu in the roots and leaves indicated that excess Cu treatments increased Cu fixation in the root cell walls, which decreased Cu mobility. Compared to HF/Mb, HF/Mp sequestered more Cu in its root cell walls and less Cu in leaf plastids, nuclei, and mitochondria. Moreover, HF/Mp roots and leaves had higher concentrations of water-insoluble Cu compounds than HF/Mb, which reduced Cu mobility and toxicity. Fourier transform infrared spectroscopy analysis showed that the carboxyl, hydroxyl and acylamino groups of the cellulose, hemicellulose, pectin and proteins were the main Cu binding sites in the root cell walls. Excess Cu-induced superoxide anion and malondialdehyde were 28.6% and 5.1% lower, but soluble phenolics, ascorbate and glutathione were 10.5%, 41.9% and 17.7% higher in HF/Mp than HF/Mb leaves. Compared with HF/Mb, certain genes involved in Cu transport were downregulated, while other genes involved in detoxification were upregulated in HF/Mp roots and leaves. Our results show that Mp inhibited Cu translocation and mitigated Cu toxicity in Malus scions by regulating Cu mobility, antioxidant defense mechanisms, and transcription of key genes involved in Cu translocation and detoxification.

Transcriptional regulation of ZIP genes is independent of local zinc status in Brachypodium shoots upon zinc deficiency and resupply

The biological processes underlying zinc homeostasis are targets for genetic improvement of crops to counter human malnutrition. Detailed phenotyping, ionomic, RNA-Seq analyses and flux measurements with ⁶⁷ Zn isotope revealed whole-plant molecular events underlying zinc homeostasis upon varying zinc supply and during zinc resupply to starved Brachypodium distachyon (Brachypodium) plants. Although both zinc deficiency and excess hindered Brachypodium growth, accumulation of biomass and micronutrients into roots and shoots differed depending on zinc supply. The zinc resupply dynamics involved 1,893 zinc-responsive genes. Multiple zinc-regulated transporter and iron-regulated transporter (IRT)-like protein (ZIP) transporter genes and dozens of other genes were rapidly and transiently down-regulated in early stages of zinc resupply, suggesting a transient zinc shock, sensed locally in roots. Notably, genes with identical regulation were observed in shoots without zinc accumulation, pointing to root-to-shoot signals mediating whole-plant responses to zinc resupply. Molecular events uncovered in the grass model Brachypodium are useful for the improvement of staple monocots.

Multivariate analysis of metals contents in spices commonly consumed in republic of Korea

Concentrations of lead (Pb), cadmium (Cd), arsenic (As), mercury (Hg), zinc (Zn), calcium (Ca), iron (Fe), nickel (Ni) and copper (Cu) were determined in 310 samples of commonly consumed spices from the market in Korea. The content of metals was assayed by acid wet digestion followed by inductively coupled plasma mass spectrometry (ICP-MS) or ICP. The content of Hg was analysed using a direct mercury analyser (DMA). Leafy spices had a significantly higher content of Pb, Cd, As, Hg, Ca and Ni when compared to those of fruit spices. Principal component analysis/cluster analysis (PCA/CA) analyses showed a high positive correlation and close proximities in the content of Pb and As in all samples, Zn and Ca in leafy spices and Cd and Zn in fruit spices.

Copper promoting oyster larval growth and settlement: Molecular insights from RNA-seq

As a cofactor of key enzymes, Cu is required in living organisms, although Cu levels in the natural environment are typically low. In this study, the promotion of growth and settlement on the larvae of oyster Crassostrea angulata was observed at an environmentally relevant concentration (10 μg/L Cu). Interestingly, Cu accumulation in the soft tissue of oyster larvae increased during the larval development and exhibited a sharp increase at the late pelagic stage. With the help of RNA-seq, we constructed a high-quality transcriptional database of the oyster C. angulata larvae (24,257 genes with an average length of 1594 bp) via de novo assembly, which provided the basic molecular changes during the larval development. Network analysis of five early developmental stages and differential expression under Cu exposure were integrated to examine the roles of Cu in oyster larvae. Our molecular analysis demonstrated that both ion channels and organic transporters contributed to Cu internalization from the external environment, including zinc transporters and amino acid transporters. The followed distribution of Cu across cells was achieved by ATP7A, the circulatory system, and the Cu transporters (CTRs). Cu exposure enhanced the ribosome and the calcium binding proteins with a higher rate of translation and shell formation, giving rise to faster growth of oyster larvae. Furthermore, Cu facilitated the settling process by upregulating the chitin binding genes and then promoting the formation of the proteinaceous matrix between larvae and substrate. Our study presents the molecular basis for Cu promotion (i.e., hormesis) effects on oyster larval growth and settlement.

Low nitrate alleviates iron deficiency by regulating iron homeostasis in apple

Iron (Fe) is an essential element for plant growth, development and metabolism. Due to its lack of solubility and low bioavailability in soil, Fe levels are usually far below the optimum amount for most plants' growth and development. In apple production, excessive use of nitrogen fertilizer may cause iron chlorosis symptoms in the newly growing leaves, but the regulatory mechanisms underlying this phenomenon are unclear. In this study, low nitrate (NO₃^- , LN) application alleviated the symptoms of Fe deficiency and promoted lower rhizosphere pH, which was beneficial for root Fe acquisition. At the same time, LN treatment increased citrate and abscisic acid accumulation in roots, which promoted Fe transport from root to shoot and maintained Fe homeostasis. Moreover, qRT-PCR analysis showed that nitrate application caused differential expression of genes related to Fe uptake and transport, as well as transcriptional regulators. In summary, our data reveal that low nitrate alleviated Fe deficiency through multiple pathways, demonstrating a new option for minimizing Fe deficiency by regulating the balance between nutrients.

Suppression of NtZIP4A/B Changes Zn and Cd Root-to-Shoot Translocation in a Zn/Cd Status-Dependent Manner

In tobacco, the efficiency of Zn translocation to shoots depends on Zn/Cd status. Previous studies pointed to the specific contribution of root parts in the regulation of this process, as well as the role of NtZIP4A/B (from the ZIP family; Zrt Irt-like Proteins). Here, to verify this hypothesis, NtZIP4A/B RNAi lines were generated. Then, in plants exposed to combinations of Zn and Cd concentrations in the medium, the consequences of NtZIP4A/B suppression for the translocation of both metals were determined. Furthermore, the apical, middle, and basal root parts were examined for accumulation of both metals, for Zn localization (using Zinpyr-1), and for modifications of the expression pattern of ZIP genes. Our results confirmed the role of NtZIP4A/B in the control of Zn/Cd-status-dependent transfer of both metals to shoots. Furthermore, they indicated that the middle and basal root parts contributed to the regulation of this process by acting as a reservoir for excess Zn and Cd. Expression studies identified several candidate ZIP genes that interact with NtZIP4A/B in the root in regulating Zn and Cd translocation to the shoot, primarily NtZIP1-like in the basal root part and NtZIP2 in the middle one.

Copper: uptake, toxicity and tolerance in plants and management of Cu-contaminated soil

Copper (Cu) is an essential mineral nutrient for the proper growth and development of plants; it is involved in myriad morphological, physiological, and biochemical processes. Copper acts as a cofactor in various enzymes and performs essential roles in photosynthesis, respiration and the electron transport chain, and is a structural component of defense genes. Excess Cu, however, imparts negative effects on plant growth and productivity. Many studies have summarized the adverse effects of excess Cu on germination, growth, photosynthesis, and antioxidant response in agricultural crops. Its inhibitory influence on mineral nutrition, chlorophyll biosynthesis, and antioxidant enzyme activity has been verified. The current review focuses on the availability and uptake of Cu by plants. The toxic effects of excess Cu on seed germination, plant growth and development, photosynthesis, and antioxidant response in plants are discussed. Plant tolerance mechanisms against Cu stress, and management of Cu-contaminated soils are presented.

Interactions between zinc and Phomopsis longicolla infection in roots of Glycine max

Phomopsis. longicolla is a hemibiotrophic fungus causing significant soybean yield loss worldwide. To reveal the role of zinc in plant-pathogen interactions, soybean seedlings were grown hydroponically with a range of Zn concentrations, 0.06 µM (deficient, Zn0), 0.4 µM (optimal growth), 1.5 µM, 4 µM, 12 µM, and toxic 38 μM, and were subsequently inoculated with P. longicolla via the roots. In vivo analysis of metal distribution in tissues by micro-X-ray fluorescence showed local Zn mobilization in the root maturation zone in all treatments. Decreased root and pod biomass, and photosynthetic performance in infected plants treated with 0.4 µM Zn were accompanied with accumulation of Zn, jasmonoyl-L-isoleucine (JA-Ile), jasmonic acid, and cell wall-bound syringic acid (cwSyA) in roots. Zn concentration in roots of infected plants treated with 1.5 µM Zn was seven-fold higher than in the 0.4 µM Zn treatment, which together with accumulation of JA-Ile, cwSyA, cell wall-bound vanilic acid and leaf jasmonates contributed to maintaining photosynthesis and pod biomass. Host-pathogen nutrient competition and phenolics accumulation limited the infection in Zn-deficient plants. The low infection rate in Zn 4 µM-treated roots correlated with salicylic and 4-hydroxybenzoic acid, and cell wall-bound p-coumaric acid accumulation. Zn toxicity promoted pathogen invasion and depleted cell wall-bound phenolics. The results show that manipulation of Zn availability improves soybean resistance to P. longicolla by stimulating phenolics biosynthesis and stress-inducible phytohormones.

1,135 ionomes reveal the global pattern of leaf and seed mineral nutrient and trace element diversity in Arabidopsis thaliana

Soil is a heterogeneous reservoir of essential elements needed for plant growth and development. Plants have evolved mechanisms to balance their nutritional needs based on availability of nutrients. This has led to genetically based variation in the elemental composition, the 'ionome', of plants, both within and between species. We explore this natural variation using a panel of wild-collected, geographically widespread Arabidopsis thaliana accessions from the 1001 Genomes Project including over 1,135 accessions, and the 19 parental accessions of the Multi-parent Advanced Generation Inter-Cross (MAGIC) panel, all with full-genome sequences available. We present an experimental design pipeline for high-throughput ionomic screenings and analyses with improved normalisation procedures to account for errors and variability in conditions often encountered in large-scale, high-throughput data collection. We report quantification of the complete leaf and seed ionome of the entire collection using this pipeline and a digital tool, Ion Explorer, to interact with the dataset. We describe the pattern of natural ionomic variation across the A. thaliana species and identify several accessions with extreme ionomic profiles. It forms a valuable resource for exploratory genetic mapping studies to identify genes underlying natural variation in leaf and seed ionome and genetic adaptation of plants to soil conditions.

Transcriptional Regulation of Genes Involved in Zinc Uptake, Sequestration and Redistribution Following Foliar Zinc Application to Medicago sativa

Zinc (Zn) is an essential micronutrient for plants and animals, and Zn deficiency is a widespread problem for agricultural production. Although many studies have been performed on biofortification of staple crops with Zn, few studies have focused on forages. Here, the molecular mechanisms of Zn transport in alfalfa (Medicago sativa L.) were investigated following foliar Zn applications. Zinc uptake and redistribution between shoot and root were determined following application of six Zn doses to leaves. Twelve putative genes encoding proteins involved in Zn transport (MsZIP1-7, MsZIF1, MsMTP1, MsYSL1, MsHMA4, and MsNAS1) were identified and changes in their expression following Zn application were quantified using newly designed RT-qPCR assays. These assays are the first designed specifically for alfalfa and resulted in being more efficient than the ones already available for Medicago truncatula (i.e., MtZIP1-7 and MtMTP1). Shoot and root Zn concentration was increased following foliar Zn applications ≥ 0.1 mg plant-1. Increased expression of MsZIP2, MsHMA4, and MsNAS1 in shoots, and of MsZIP2 and MsHMA4 in roots was observed with the largest Zn dose (10 mg Zn plant-1). By contrast, MsZIP3 was downregulated in shoots at Zn doses ≥ 0.1 mg plant-1. Three functional gene modules, involved in Zn uptake by cells, vacuolar Zn sequestration, and Zn redistribution within the plant, were identified. These results will inform genetic engineering strategies aimed at increasing the efficiency of crop Zn biofortification.

Leveraging computational genomics to understand the molecular basis of metal homeostasis

Genome-based data is helping to reveal the diverse strategies plants and algae use to maintain metal homeostasis. In addition to acquisition, distribution and storage of metals, acclimating to feast or famine can involve a wealth of genes that we are just now starting to understand. The fast-paced acquisition of genome-based data, however, is far outpacing our ability to experimentally characterize protein function. Computational genomic approaches are needed to fill the gap between what is known and unknown. To avoid misconstruing bioinformatically derived data, which is the root cause of the inaccurate functional annotations that plague databases, functional inferences from diverse sources and contextualization of that evidence with a robust understanding of protein family evolution is needed. Phylogenomic- and comparative-genomic-based studies can aid in the interpretation of experimental data or provide a spark for the discovery of a new function. These analyses not only lead to novel insight into a target protein's function but can generate thought-provoking insights across protein families.

Copper uptake, essentiality, toxicity, detoxification and risk assessment in soil-plant environment

Copper (Cu) is an essential metal for human, animals and plants, although it is also potentially toxic above supra-optimal levels. In plants, Cu is an essential cofactor of numerous metalloproteins and is involved in several biochemical and physiological processes. However, excess of Cu induces oxidative stress inside plants via enhanced production of reactive oxygen species (ROS). Owing to its dual nature (essential and a potential toxicity), this metal involves a complex network of uptake, sequestration and transport, essentiality, toxicity and detoxification inside the plants. Therefore, it is vital to monitor the biogeo-physiochemical behavior of Cu in soil-plant-human systems keeping in view its possible essential and toxic roles. This review critically highlights the latest understanding of (i) Cu adsorption/desorption in soil (ii) accumulation in plants, (iii) phytotoxicity, (iv) tolerance mechanisms inside plants and (v) health risk assessment. The Cu-mediated oxidative stress and resulting up-regulation of several enzymatic and non-enzymatic antioxidants have been deliberated at molecular and cellular levels. Moreover, the role of various transporter proteins in Cu uptake and its proper transportation to target metalloproteins is critically discussed. The review also delineates Cu build-up in plant food and accompanying health disorders. Finally, this review proposes some future perspectives regarding Cu biochemistry inside plants. The review, to a large extent, presents a complete picture of the biogeo-physiochemical behavior of Cu in soil-plant-human systems supported with up-to-date 10 tables and 5 figures. It can be of great interest for post-graduate level students, scientists, industrialists, policymakers and regulatory authorities.

Micronutrient homeostasis and chloroplast iron protein expression is largely maintained in a chloroplast copper transporter mutant

PAAI is a P-Type ATPase that functions to import copper (Cu) into the chloroplast. Arabidopsis thaliana (L.) Heynh. paa1 mutants have lowered plastocyanin levels, resulting in a decreased photosynthetic electron transport rate. In nature, iron (Fe) and Cu homeostasis are often linked and it can be envisioned that paa1 acclimates its photosynthetic machinery by adjusting expression of its chloroplast Fe-proteome, but outside of Cu homeostasis paa1 has not been studied. Here, we characterise paa1 ultrastructure and accumulation of electron transport chain proteins in a paa1 allelic series. Furthermore, using hydroponic growth conditions, we characterised metal homeostasis in paa1 with an emphasis on the effects of Fe deficiency. Surprisingly, the paa1 mutation does not affect chloroplast ultrastructure or the accumulation of other photosynthetic electron transport chain proteins, despite the strong decrease in electron transport rate. The regulation of Fe-related photosynthetic electron transport proteins in response to Fe status was maintained in paa1, suggesting that regulation of the chloroplast Fe proteins ignores operational signals from photosynthetic output. The characterisation of paa1 has revealed new insight into the regulation of expression of the photosynthetic electron transport chain proteins and chloroplast metal homeostasis and can help to develop new strategies for the detection of shoot Fe deficiency.

Manganese Treatment Alleviates Zinc Deficiency Symptoms in Arabidopsis Seedlings

Plant phenotypes caused by mineral deficiencies differ depending on growth conditions. We recently reported that the growth of Arabidopsis thaliana was severely inhibited on MGRL-based zinc (Zn)-deficient medium but not on Murashige-Skoog-based Zn-deficient medium. Here, we explored the underlying reason for the phenotypic differences in Arabidopsis grown on the different media. The root growth and chlorophyll contents reduced by Zn deficiency were rescued by the addition of extra manganese (Mn) during short-term growth (10 or 14 d). However, this treatment did not affect the growth recovery after long-term growth (38 d). To investigate the reason for plant recovery from Zn deficiency, we performed the RNA-seq analysis of the roots grown on the Zn-basal medium and the Zn-depleted medium with/without additional Mn. Principal component analysis of the RNA-seq data showed that the gene expression patterns of plants on the Zn-basal medium were similar to those on the Zn-depleted medium with Mn, whereas those on the Zn-depleted medium without Mn were different from the others. The expression of several transcription factors and reactive oxygen species (ROS)-related genes was upregulated in only plants on the Zn-depleted medium without Mn. Consistent with the gene expression data, ROS accumulation in the roots grown on this medium was higher than those grown in other conditions. These results suggest that plants accumulate ROS and reduce their biomass under undesirable growth conditions, such as Zn depletion. Taken together, this study shows that the addition of extra Mn to the Zn-depleted medium induces transcriptional changes in ROS-related genes, thereby alleviating short-term growth inhibition due to Zn deficiency.

Complex gene regulation between young and old soybean leaves in responses to manganese toxicity

Manganese (Mn) is an essential micronutrient for plant growth. However, excess manganese is toxic and inhibits crop production. Although it is widely known that physiological and molecular mechanisms underlie plant responses to Mn toxicity, few studies have been conducted to compare Mn tolerance capabilities between young and old leaves in plants; thus, the mechanisms underlying Mn tolerance in different plant tissues or organs are not fully understood. In this study, the dose responses of soybean to Mn availability were investigated. Genome-wide transcriptomic analysis was subsequently conducted to identify the differentially expressed genes (DEGs) in both young and old leaves of soybean in responses to Mn toxicity. Our results showed that excess Mn severely inhibited soybean growth and increased both Mn accumulation in and brown spots on soybean leaves, especially for the old leaves, strongly suggesting that more Mn was allocated to old leaves in soybean. Transcriptomic profiling revealed that totals of 4410 and 2258 DEGs were separately identified in young leaves and old leaves. Furthermore, only 944 DEGs were found to be commonly regulated in both young and old leaves of soybean, strongly suggesting distinct responses present in soybean young and old leaves in responses to Mn toxicity.

Evaluating the potential use of Cu-contaminated soils for giant reed (Arundo donax, L.) cultivation as a biomass crop

Over the past decades, the important topic of environmental sustainability, impact, and security of the fossil fuel supply has stimulated interest in using lignocellulosic feedstocks as biofuel to partially cover energy demands. Among energy no-food crops, giant reed (Arundo donax, L.), a perennial rhizomatous grass has been identified as a leading candidate crop for lignocellulosic feedstock, due to its positive energy balance, and low ecological/agro-management demands. The aim of the present study was to characterize the physiological response of Arundo donax (L.) to artificial soil contamination with three different Cu levels (200, 400, and 800 ppm), and to assess the relationship between plant Cu tolerance and S assimilation rate. The present study not only confirms the ability of Arundo donax L. to cope with Cu stress and therefore to grow in marginal, degraded lands abandoned by mainstream agricultural, but also shows that plant performance might be likely ascribed to a modulation of sulfate metabolism resulting in increased thiols content.

Zn/Cd status-dependent accumulation of Zn and Cd in root parts in tobacco is accompanied by specific expression of ZIP genes

BACKGROUND

Root-to-shoot translocation of zinc (Zn) and cadmium (Cd) depends on the concentrations of both metals in the medium. A previous study on tobacco (Nicotiana tabacum) pointed to the contribution of NtZIP1, NtZIP2, NtZIP4 and NtIRT1-like in the regulation of this phenomenon. To learn more, Zn and Cd accumulation, root/shoot distribution and the expression of ZIP genes were investigated in the apical, middle and basal root parts.

RESULTS

We show that Zn/Cd status-dependent root-shoot distribution of both metals was related to distinct metal accumulation in root parts. At low Zn and Cd in the medium, the apical part contained the highest metal level; at higher concentrations, the middle and basal parts were the major sink for excess metal. The above were accompanied by root part-specific expression pattern modifications of ZIPs (NtZIP1-like, NtZIP2, NtZIP4A/B, NtZIP5A/B, NtZIP5-like, NtZIP8, NtZIP11, NtIRT1, and NtIRT1-like) that fell into four categories with respect to the root part. Furthermore, for lower Zn/Cd concentrations changes were noted for NtZIP5A/B and NtZIP5-like only, but at higher Zn and Cd levels for NtZIP1-like, NtZIP5-like, NtZIP8, NtZIP11, NtIRT1, and NtIRT1-like. NtZIP1, here renamed to NtZIP5B, was cloned and characterized. We found that it was a zinc deficiency-inducible transporter involved in zinc and cadmium uptake from the soil solution primarily by the middle root part.

CONCLUSIONS

We conclude that regulation of the longitudinal distribution of Zn and Cd is highly specific, and that the apical, middle and basal root parts play distinct roles in Zn/Cd status-dependent control of metal translocation efficiency to shoots, including the stimulation of Zn translocation to shoots in the presence of Cd. These results provide new insight into the root part-specific unique role of NtZIP5B and other ZIP genes in the longitudinal distribution of zinc and cadmium and their contribution to the regulation of root-to-shoot translocation.