Redundant roles of four ZIP family members in zinc homeostasis and seed development in Arabidopsis thaliana

Specific redox and iron homeostasis responses in the root tip of Arabidopsis upon zinc excess

Zinc (Zn) excess negatively impacts primary root growth in Arabidopsis thaliana. Yet, the effects of Zn excess on specific growth processes in the root tip (RT) remain largely unexplored. Transcriptomics, ionomics, and metabolomics were used to examine the specific impact of Zn excess on the RT compared with the remaining root (RR). Zn excess exposure resulted in a shortened root apical meristem and elongation zone, with differentiation initiating closer to the tip of the root. Zn accumulated at a lower concentration in the RT than in the RR. This pattern was associated with lower expression of Zn homeostasis and iron (Fe) deficiency response genes. A distinct distribution of Zn and Fe in RT and RR was highlighted by laser ablation inductively coupled plasma-mass spectrometry analysis. Specialized tryptophan (Trp)-derived metabolism genes, typically associated with redox and biotic stress responses, were specifically upregulated in the RT upon Zn excess, among those Phytoalexin Deficient 3 (PAD3) encoding the last enzyme of camalexin synthesis. In the roots of wild-type seedlings, camalexin concentration increased by sixfold upon Zn excess, and a pad3 mutant displayed increased Zn sensitivity and an altered ionome. Our results indicate that distinct redox and iron homeostasis mechanisms are key elements of the response to Zn excess in the RT.

Changing paradigms for the micronutrient zinc, a known protein cofactor, as a signal relaying also cellular redox state

The micronutrient zinc (Zn) is often poorly available but toxic when present in excess, so a tightly controlled Zn homoeostasis network operates in all organisms. This review summarizes our present understanding of plant Zn homoeostasis. In Arabidopsis, about 1,900 Zn-binding metalloproteins require Zn as a cofactor. Abundant Zn metalloproteins reside in plastids, mitochondria and peroxisomes, emphasizing the need to address how Zn reaches these proteins. Apo-Zn metalloproteins do not acquire Zn2+ from a cytosolic pool of free cations, but instead through associative ligand exchange from Zn-buffering molecules. The importance of cytosolic thiols in Zn buffering suggests that, besides elevated Zn influx, a more oxidized redox state is also predicted to cause elevated labile-bound Zn levels, consistent with the suppression of a Zn deficiency marker under oxidative stress. Therefore, we consider a broadened physiological scope in plants for a possible signalling role of Zn2+, experimentally supported only in animals to date.

Plasma membrane-associated calcium signaling modulates zinc homeostasis in Arabidopsis

Zinc (Zn) is a crucial micronutrient for all organisms, and its deficiency can significantly hamper crop yield and quality. However, the understanding of the regulatory mechanisms involved in plant Zn signal perception and transduction remains limited. In this study, we discovered that the Ca2+-CBL1/4/5/8/9-CIPK3/9/23/26-ZIP12 signaling module effectively responds to Zn deficiency and regulates Zn homeostasis in Arabidopsis thaliana. Furthermore, we determined that CIPK3/9/23/26 interact with the Zn transporter ZIP12 and phosphorylate it primarily at Ser185. This phosphorylation event was crucial for the stability of the ZIP12 protein, suggesting that it regulates the function of ZIP12 in Zn transport. Collectively, our findings identify a plasma membrane-associated calcium signaling pathway that regulates Zn homeostasis in Arabidopsis thaliana. This pathway represents a promising target for molecular breeding approaches aimed at developing crops with enhanced tolerance to Zn deficiency.

Arabidopsis thaliana Zn transporter genes ZIP3 and ZIP5 provide the main Zn uptake route and act redundantly to face Zn deficiency

In response to Zn deficiency, plants are thought to adjust Zn homeostasis through the coordinated expression of Zn transporters. Zn transporters are identified in the ZIP, HMA and CDF families of cation transporters, although only few are characterized. We determined gene expression over time, root-specific location of expression and phenotypes of single and double loss-of-function mutants of several Arabidopsis thaliana transporters, known to be induced by Zn deficiency. Transcription of Zn transporter genes is induced in the first 6 h of exposure to Zn deficiency. ZIP1 is predominantly expressed in the endodermis and stele, ZIP3 and ZIP5 in the epidermis and cortex, IRT3 from epidermis to stele and HMA2 in xylem parenchyma. ZIP3 and ZIP5 act redundantly, with the double-mutant zip3zip5 showing high sensitivity to Zn deficiency with low biomass production, expression of other transporter genes, low Zn uptake and increased metal translocation. The root expression map and timing indicate that Zn transporters act complementary in a concerted action to control Zn homeostasis. The lack of strong Zn-deficient phenotypes in single mutants suggests a high level of functional redundancy, best illustrated for ZIP3 and ZIP5.

Copper excess transcriptional responses in roots of grapevine (Vitis sp.) rootstocks

Copper (Cu) is an essential element for plants, participating in photosynthesis, oxidative metabolism and cell wall synthesis. However, excessive Cu may become toxic, as Cu participates in Fenton chemistry and cause oxidative stress. Grapevine (Vitis sp.) is an important perennial crop, used for in natura consumption as well as for wine and juice. Vineyards are susceptible to fungal diseases that are commonly controlled by using Cu-based fungicides, which can lead to Cu accumulation in the soil. Since grape production is based on grafting scions of consumed-friendly varieties onto rootstocks that can withstand soil-borne diseases and stresses, it is important to identify rootstock genotypes that are tolerant to Cu excess. In this work, we compared physiological and molecular responses of four Vitis sp. rootstock genotypes to Cu excess, namely IAC, IBCA, Paulsen and Isabel. While IAC, IBCA, Paulsen were similarly tolerant, Isabel was the most sensitive to Cu excess. IAC and IBCA showed higher Cu accumulation in shoots, suggesting distinct partitioning strategy. We identified core Cu excess-responsive genes in grapevine roots of all four genotypes, including a putative HMA vacuolar Cu transporter and Cu-binding proteins. Genes related to the homeostasis of other elements are altered, such as iron (Fe) and phosphorus (P), suggesting that Cu excess alters the ionome balance. IAC and IBCA had extensive changes in their laccase gene repertoire, suggesting that could be related to the distinct Cu partitioning. Moreover, genes associated specifically with Isabel could be related to the genotype Cu excess sensitivity. Our work provides a valuable dataset for understanding variation in Cu tolerance how roots respond transcriptionally to Cu stress, and provide candidate genes for engineering Cu tolerance in grapevines.

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.

Zinc/Iron-Regulated Transporter-like Protein CsZIP4 Enhances Zinc and Nitrogen Uptake and Alleviates Zinc Stresses with Nitrogen Supply in Camellia sinensis

Zinc (Zn) and nitrogen (N) are the two crucial nutrients for tea plant growth and development and contribute to the quality formation of tea fresh leaves. In this study, a zinc/iron-regulated transporter-like protein 4 gene (i.e., CsZIP4) was functionally characterized. Expression profiling showed that CsZIP4 could be induced by Zn stresses and a N deficiency. Heterologous expression of CsZIP4 in yeast revealed that CsZIP4 possessed the capacity for Zn transport but not ammonium. Moreover, CsZIP4 overexpression in Arabidopsis thaliana promoted Zn and N uptake and transport and contributed to alleviate Zn stresses by collaborating with N supply, which might be interrelated to the expression of N or Zn metabolism-related genes, such as AtNRT1.1 and AtZIP4. Additionally, CsZIP4 was localized in the plasma membrane and chloroplast, which was helpful in maintaining cellular homeostasis under a Zn excess. Furthermore, silencing of CsZIP4 in tea plants by virus-induced gene silencing increased the chlorophyll content but decreased the Zn content. Finally, the yeast one-hybrid assay demonstrated that CsbZIP2 bound to the CsZIP4 promoter. These results will shed light on the functions of CsZIP4 in the N and Zn interaction in tea plants.

Localization of the MTP4 transporter to trans-Golgi network in pollen tubes of Arabidopsis thaliana

Zinc (Zn) is an essential element for plants. Numerous proteins in different cellular compartments require Zn for their structure and function. Zn can be toxic when it accumulates in high levels in the cytoplasm. Therefore, Zn homeostasis at tissue, cell, and organelle levels is vital for plant growth. A part of the metal tolerance protein (MTP) / Cation Diffusion Facilitator (CDF) transporters functions as Zn transporters, exporting Zn from the cytosol to various membrane compartments. In Arabidopsis thaliana, MTP1, MTP2, MTP3, MTP4, MTP5, and MTP12 are classified as Zn transporters (Zn-CDF). In this study, we systematically analyzed the localization of GFP-fused Zn-CDFs in the leaf epidermal cells of Nicotiana benthamiana. As previously reported, MTP1 and MTP3 were localized to tonoplast, MTP2 to endoplasmic reticulum, and MTP5 to Golgi. In addition, we identified the localization of MTP4 to trans-Golgi Network (TGN). Since MTP4 is specifically expressed in pollen, we analyzed the localization of MTP4-GFP in the Arabidopsis pollen tubes and confirmed that it is in the TGN. We also showed the Zn transport capability of MTP4 in yeast cells. We then analyzed the phenotype of an mtp4 T-DNA insertion mutant under both limited and excess Zn conditions. We found that their growth and fertility were not largely different from the wild-type. Our study has paved the way for investigating the possible roles of MTP4 in metallating proteins in the secretory pathway or in exporting excess Zn through exocytosis. In addition, our system of GFP-fused MTPs will help study the mechanisms for targeting transporters to specific membrane compartments.

Plant-microbe interactions in the rhizosphere for smarter and more sustainable crop fertilization: the case of PGPR-based biofertilizers

Biofertilizers based on plant growth promoting rhizobacteria (PGPR) are nowadays gaining increasingly attention as a modern tool for a more sustainable agriculture due to their ability in ameliorating root nutrient acquisition. For many years, most research was focused on the screening and characterization of PGPR functioning as nitrogen (N) or phosphorus (P) biofertilizers. However, with the increasing demand for food using far fewer chemical inputs, new investigations have been carried out to explore the potential use of such bacteria also as potassium (K), sulfur (S), zinc (Zn), or iron (Fe) biofertilizers. In this review, we update the use of PGPR as biofertilizers for a smarter and more sustainable crop production and deliberate the prospects of using microbiome engineering-based methods as potential tools to shed new light on the improvement of plant mineral nutrition. The current era of omics revolution has enabled the design of synthetic microbial communities (named SynComs), which are emerging as a promising tool that can allow the formulation of biofertilizers based on PGPR strains displaying multifarious and synergistic traits, thus leading to an increasingly efficient root acquisition of more than a single essential nutrient at the same time. Additionally, host-mediated microbiome engineering (HMME) leverages advanced omics techniques to reintroduce alleles coding for beneficial compounds, reinforcing positive plant-microbiome interactions and creating plants capable of producing their own biofertilizers. We also discusses the current use of PGPR-based biofertilizers and point out possible avenues of research for the future development of more efficient biofertilizers for a smarter and more precise crop fertilization. Furthermore, concerns have been raised about the effectiveness of PGPR-based biofertilizers in real field conditions, as their success in controlled experiments often contrasts with inconsistent field results. This discrepancy highlights the need for standardized protocols to ensure consistent application and reliable outcomes.

Metal Transport Systems in Plants

Plants take up metals, including essential micronutrients [iron (Fe), copper (Cu), zinc (Zn), and manganese (Mn)] and the toxic heavy metal cadmium (Cd), from soil and accumulate these metals in their edible parts, which are direct and indirect intake sources for humans. Multiple transporters belonging to different families are required to transport a metal from the soil to different organs and tissues, but only a few of them have been fully functionally characterized. The transport systems (the transporters required for uptake, translocation, distribution, redistribution, and their regulation) differ with metals and plant species, depending on the physiological roles, requirements of each metal, and anatomies of different organs and tissues. To maintain metal homeostasis in response to spatiotemporal fluctuations of metals in soil, plants have developed sophisticated and tightly regulated mechanisms through the regulation of transporters at the transcriptional and/or posttranscriptional levels. The manipulation of some transporters has succeeded in generating crops rich in essential metals but low in Cd accumulation. A better understanding of metal transport systems will contribute to better and safer crop production.

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.

Metal tolerance protein CsMTP4 has dual functions in maintaining zinc homeostasis in tea plant

Plants have evolved a series of zinc (Zn) homeostasis mechanisms to cope with the fluctuating Zn in the environment. How Zn is taken up, translocated and tolerate by tea plant remains unknown. In this study, on the basis of RNA-Sequencing, we isolated a plasma membrane-localized Metal Tolerance Protein (MTP) family member CsMTP4 from Zn-deficient tea plant roots and investigated its role in regulation of Zn homeostasis in tea plant. Heterologous expression of CsMTP4 specifically enhanced the tolerance of transgenic yeast to Zn excess. Moreover, overexpression of CsMTP4 in tea plant hairy roots stimulated Zn uptake under Zn deficiency. In addition, CsMTP4 promoted the growth of transgenic Arabidopsis plants by translocating Zn from roots to shoots under Zn deficiency and conferred the tolerance to Zn excess by enhancing the efflux of Zn from root cells. Transcriptome analysis of the CsMTP4 transgenic Arabidopsis found that the expression of Zn metabolism-related genes were differentially regulated compared with wild-type plants when exposed to Zn deficiency and excess conditions. This study provides a mechanistic understanding of Zn uptake and translocation in plants and a new strategy to improve phytoremediation efficiency.

Reduced expression of bZIP19 and bZIP23 increases zinc and cadmium accumulation in Arabidopsis halleri

Zinc is an essential micronutrient for all living organisms. When challenged by zinc-limiting conditions, Arabidopsis thaliana plants use a strategy centered on two transcription factors, bZIP19 and bZIP23, to enhance the expression of several zinc transporters to improve their zinc uptake capacity. In the zinc and cadmium hyperaccumulator plant Arabidopsis halleri, highly efficient root-to-shoot zinc translocation results in constitutive local zinc deficiency in roots and in constitutive high expression of zinc deficiency-responsive ZIP genes, supposedly boosting zinc uptake and accumulation. Here, to disrupt this process and to analyze the functions of AhbZIP19, AhbZIP23 and their target genes in hyperaccumulation, the genes encoding both transcriptional factors were knocked down using artificial microRNAs (amiRNA). Although AhbZIP19, AhbZIP23, and their ZIP target genes were downregulated, amiRNA lines surprisingly accumulated more zinc and cadmium compared to control lines in both roots and shoot driving to shoot toxicity symptoms. These observations suggested the existence of a substitute metal uptake machinery in A. halleri to maintain hyperaccumulation. We propose that the iron uptake transporter AhIRT1 participates in this alternative pathway in A. halleri.

Functional characterization of Fagopyrum tataricum ZIP gene family as a metal ion transporter

The zinc/iron-regulated transporter-like proteins (ZIP) family acts as an important transporter for divalent metal cations such as Zn, Fe, Mn, Cu, and even Cd. However, their condition is unclear in Tartary buckwheat (Fagopyrum tataricum). Here, 13 ZIP proteins were identified and were predicted to be mostly plasma membrane-localized. The transient expressions of FtZIP2 and FtZIP6 in tobacco confirmed the prediction. Multiple sequence alignment analysis of FtZIP proteins revealed that most of them had 8 putative transmembrane (TM) domains and a variable region rich in histidine residues between TM3 and TM4, indicating the reliable affinity to metal ions. Gene expression analysis by qRT-PCR showed that FtZIP genes were markedly different in different organs, such as roots, stems, leaves, flowers, fruits and seeds. However, in seedlings, the relative expression of FtZIP10 was notably induced under the CdCl2 treatment, while excessive Zn2+, Fe2+, Mn2+ and Cd2+ increased the transcript of FtZIP5 or FtZIP13, in comparison to normal conditions. Complementation of yeast mutants with the FtZIP family genes demonstrate that FtZIP7/10/12 transport Zn, FtZIP5/6/7/9/10/11 transport Fe, FtZIP12 transports Mn and FtZIP2/3/4/7 transport Cd. Our data suggest that FtZIP proteins have conserved functions of transportation of metal ions but with distinct spatial expression levels.

AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters of Arabidopsis thaliana L

The mainstream of the post-genome target-assisted breeding in crop plant species includes biofortification such as high-throughput phenotyping along with genome-based selection. Therefore, in this work, we used the Web-service Plant_SNP_TATA_Z-tester, which we have previously developed, to run a uniform in silico analysis of the transcriptional alterations of 54,013 protein-coding transcripts from 32,833 Arabidopsis thaliana L. genes caused by 871,707 SNPs located in the proximal promoter region. The analysis identified 54,993 SNPs as significantly decreasing or increasing gene expression through changes in TATA-binding protein affinity to the promoters. The existence of these SNPs in highly conserved proximal promoters may be explained as intraspecific diversity kept by the stabilizing natural selection. To support this, we hand-annotated papers on some of the Arabidopsis genes possessing these SNPs or on their orthologs in other plant species and demonstrated the effects of changes in these gene expressions on plant vital traits. We integrated in silico estimates of the TBP-promoter affinity in the AtSNP_TATAdb knowledge base and showed their significant correlations with independent in vivo experimental data. These correlations appeared to be robust to variations in statistical criteria, genomic environment of TATA box regions, plants species and growing conditions.

TaNRAMP3 is essential for manganese transport in Triticum aestivum

Manganese (Mn) is an essential trace element for almost all living organisms. In plants, Mn deficiency, which is occurs in calcareous soils or alkaline soils, severely limiting crop yields. However, the potential mechanism of Mn transport in Triticum aestivum is still obscure. Here, we found that TaNRAMP3, a member of the naturally resistant macrophage protein (NRAMP) family in Triticum aestivum, is located in the plasma membrane of protoplasts and functions as an influx transporter for Mn in yeast (Δsmf1). The expression of TaNRAMP3 was induced under Mn-deficiency conditions. Furthermore, TaNRAMP3-RNAi plants exhibited a sensitive phenotype, while transgenic plants overexpressing TaNRAMP3 showed a tolerant phenotype. In addition, TaNRAMP3 rescued the sensitive phenotype of Arabidopsis nramp1 mutant under Mn deficiency condition. In summary, our study reveals the key role of TaNRAMP3 in Mn transport in Triticum aestivum, allowing it to adapt to Mn-deficiency stress. These findings provide new insights for the cultivation of Mn-deficiency tolerant wheat varieties.

Nutrient carriers at the heart of plant nutrition and sensing

Plants require water and several essential nutrients for their development. The radial transport of nutrients from the soil to the root vasculature is achieved through a combination of three different pathways: apoplastic, symplastic, and transcellular. A common feature for these pathways is the requirement of carriers to transport nutrients across the plasma membrane. An efficient transport of nutrients across the root cell layers relies on a large number of carriers, each of them having their own substrate specificity, tissular and subcellular localization. Polarity is also emerging as a major feature allowing their function. Recent advances on radial transport of nutrients, especially carrier mediated nutrient transport will be discussed in this review, as well as the role of transporters as nutrient sensors.

Physiological and molecular mechanisms of medicinal plants in response to cadmium stress: Current status and future perspective

Medicinal plants have a wide range of uses worldwide. However, the quality of medicinal plants is affected by severe cadmium pollution. Cadmium can reduce photosynthetic capacity, lead to plant growth retardation and oxidative stress, and affect secondary metabolism. Medicinal plants have complex mechanisms to cope with cadmium stress. On the one hand, an antioxidant system can effectively scavenge excess reactive oxygen species produced by cadmium stress. On the other hand, cadmium chelates are formed by chelating peptides and then sequestered through vacuolar compartmentalization. Cadmium has no specific transporter in plants and is generally transferred to plant tissues through competition for the transporters of divalent metal ions, such as zinc, iron, and manganese. In recent years, progress has been achieved in exploring the physiological mechanisms by which medicinal plants responding to cadmium stress. The exogenous regulation of cadmium accumulation in medicinal plants has been studied, and the aim is reducing the toxicity of cadmium. However, research into molecular mechanisms is still lagging. In this paper, we review the physiological and molecular mechanisms and regulatory networks of medicinal plants exposed to cadmium, providing a reference for the study on the responses of medicinal plants to cadmium stress.

Ferrous iron uptake via IRT1/ZIP evolved at least twice in green plants

Iron (Fe) is essential for virtually all organisms, being irreplaceable because of its electrochemical properties that enable many biochemical processes, including photosynthesis. Besides its abundance, Fe is generally found in the poorly soluble form of ferric iron (Fe³⁺ ), while most plants uptake the soluble form Fe²⁺ . The model angiosperm Arabidopsis thaliana, for example, captures Fe through a mechanism that lowers rhizosphere pH through proton pumping that increases Fe³⁺ solubility, which is then reduced by a membrane-bound reductase and transported into the cell by the zinc-regulated, iron-regulated transporter-like protein (ZIP) family protein AtIRT1. ZIP proteins are transmembrane transporters of divalent metals such as Fe²⁺ , Zn²⁺ , Mn²⁺ , and Cd²⁺ . In this work, we investigated the evolution of functional homologs of IRON-REGULATED TRANSPORTER 1/ZIP in the supergroup Archaeplastida (Viridiplantae + Rhodophyta + Glaucophyta) using 51 genomes of diverse lineages. Our analyses suggest that Fe is acquired through deeply divergent ZIP proteins in land plants and chlorophyte green algae, indicating that Fe²⁺ uptake by ZIP proteins evolved independently at least twice throughout green plant evolution. Our results indicate that the archetypical IRON-REGULATED TRANSPORTER (IRT) proteins from angiosperms likely emerged before the origin of land plants during early streptophyte algae terrestrialization, a process that required the evolution of Fe acquisition in terrestrial subaerial settings.

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.

Biofortification of common bean (Phaseolus vulgaris L.) with iron and zinc: Achievements and challenges

Micronutrient deficiencies (hidden hunger), particularly in iron (Fe) and zinc (Zn), remain one of the most serious public health challenges, affecting more than three billion people globally. A number of strategies are used to ameliorate the problem of micronutrient deficiencies and to improve the nutritional profile of food products. These include (i) dietary diversification, (ii) industrial food fortification and supplements, (iii) agronomic approaches including soil mineral fertilisation, bioinoculants and crop rotations, and (iv) biofortification through the implementation of biotechnology including gene editing and plant breeding. These efforts must consider the dietary patterns and culinary preferences of the consumer and stakeholder acceptance of new biofortified varieties. Deficiencies in Zn and Fe are often linked to the poor nutritional status of agricultural soils, resulting in low amounts and/or poor availability of these nutrients in staple food crops such as common bean. This review describes the genes and processes associated with Fe and Zn accumulation in common bean, a significant food source in Africa that plays an important role in nutritional security. We discuss the conventional plant breeding, transgenic and gene editing approaches that are being deployed to improve Fe and Zn accumulation in beans. We also consider the requirements of successful bean biofortification programmes, highlighting gaps in current knowledge, possible solutions and future perspectives.

The Role of Membrane Transporters in the Biofortification of Zinc and Iron in Plants

Over three billion people suffer from various health issues due to the low supply of zinc (Zn) and iron (Fe) in their food. Low supply of micronutrients is the main cause of malnutrition and biofortification could help to solve this issue. Understanding the molecular mechanisms of biofortification is challenging. The membrane transporters are involved in the uptake, transport, storage, and redistribution of Zn and Fe in plants. These transporters are also involved in biofortification and help to load the Zn and Fe into the endosperm of the seeds. Very little knowledge is available on the role and functions of membrane transporters involved in seed biofortification. Understanding the mechanism and role of membrane transporters could be helpful to improve biofortification. In this review, we provide the details on membrane transporters involved in the uptake, transport, storage, and redistribution of Zn and Fe. We also discuss available information on transporters involved in seed biofortification. This review will help plant breeders and molecular biologists understand the importance and implications of membrane transporters for seed biofortification.

QTL analysis and candidate gene prediction for seed density per silique by QTL-seq and RNA-seq in spring Brassica napus L

Seed density per silique (SD) is an important agricultural trait and plays an important role in the yield performance of Brassica napus L. (B. napus). In this study, a genetic linkage map was constructed using a double haploid (DH) population with 213 lines derived from a cross between a low SD line No. 935 and a high SD line No. 3641, and a total of 1,098,259 SNP (single-nucleotide polymorphisms) markers and 2,102 bins were mapped to 19 linkage groups. Twenty-eight QTLs for SD were detected on chromosomes A02, A04, A05, A09, C02, C03, C06, and C09 of B. napus, of which eight QTLs were on chromosome A09 and explained 5.89%-13.24% of the phenotypic variation. Furthermore, a consistent QTL for SD on chromosome A09, cqSD-A9a, was identified in four environments by QTL meta-analysis, explaining 10.68% of the phenotypic variation. In addition, four pairs of epistatic interactions were detected in the DH population via QTL epistasis analysis, indicating that SD is controlled not only by additive effects but also by epistatic effects that play an important role in spring B. napus., but with little environmental effect. Moreover, 18 closely linked SSR markers for cqSD-A9a were developed, as a result, it was mapped to a 1.86Mb (7.80-9.66 Mb) region on chromosome A09. A total of 13 differentially expressed genes (DEGs) were screened in the candidate interval by RNA-seq analysis, which were differentially expressed in buds, leaves and siliques both between and siliques both between two parents and two pools of extremely high-SD and low-SD lines in the DH population. Three of 13 DEGs were possible candidate genes that might control SD: BnaA09g14070D, which encodes a callose synthase that plays an important role in development and stress responses; BnaA09g14800D, a plant synaptic protein that encodes a membrane component; and BnaA09g18250D, which is responsible for DNA binding, transcriptional regulation, and sequence-specific DNA binding and is involved in the response to growth hormone stimulation. Overall, these results lay a foundation for fine mapping and gene cloning for SD in B. napus.

Characterization of zinc uptake and translocation visualized with positron-emitting 65Zn tracer and analysis of transport-related gene expression in two Lotus japonicus accessions

BACKGROUND AND AIMS

Zinc (Zn) is an essential element for humans and plants. However, Zn deficiency is widespread and 25 % of the world's population is at risk of Zn deficiency. To overcome the deficiency of Zn intake, crops with high Zn content are required. However, most crop-producing areas have Zn-deficient soils, therefore crops with excellent Zn uptake/transport characteristics (i.e. high Zn efficiency) are needed. Our objective was to identify the crucial factors responsible for high Zn efficiency in the legume Lotus japonicus.

METHODS

We evaluated Zn efficiency by static and real-time visualization of radioactive Zn (65Zn) uptake/transport in two L. japonicus accessions, MG-20 and B-129, that differ in Zn efficiency. The combination of visualization methods verified the dynamics of Zn accumulation and transport within the plant. We compared gene expression under a normal Zn concentration (control) and Zn deficiency to evaluate genetic factors that may determine the differential Zn efficiency of the accessions.

KEY RESULTS

The accession B-129 accumulated almost twice the amount of Zn as MG-20. In the static 65Zn images, 65Zn accumulated in meristematic tissues, such as root tips and the shoot apex, in both accessions. The positron-emitting tracer imaging system (PETIS), which follows the transport process in real time, revealed that 65Zn transport to the shoot was more rapid in B-129 than in MG-20. Many genes associated with Zn uptake and transport were more highly expressed in B-129 than in MG-20 under the control condition. These gene expression patterns under Zn deficiency differed from those under the control Zn condition.

CONCLUSIONS

PETIS confirmed that the real-time transport of 65Zn to the shoot was faster in B-129 than in MG-20. The high Zn efficiency of B-129 may be due to the elevated expression of a suite of Zn uptake- and transport-related genes.

Fungal Zinc Homeostasis and Its Potential as an Antifungal Target: A Focus on the Human Pathogen Aspergillus fumigatus

Aspergillus fumigatus is an opportunistic airborne fungus that causes severe invasive aspergillosis in immunocompromised patients. Zinc is an essential micronutrient for the growth of A. fumigatus and even for all microorganisms. An increasing number of studies have reported that fungal zinc acquisition ability plays a key role in fungal survival in hosts with an extremely zinc-limited microenvironment. The ability to fight scarcity and excess of zinc are tightly related to fungal virulence and may be used as new potential targets. Because the regulation of zinc homeostasis is important, a thorough understanding of the functional genes involved in the regulatory network for zinc homeostasis is required for fungal pathogens. The current mini-review summarized potential zinc homeostasis regulators in A. fumigatus and classified these regulators according to localization and function, which were identified or predicted based on A. fumigatus or deduced from homologs in model yeasts. Future perspectives for zinc homeostasis regulators as potential antifungal targets to treat invasive aspergillosis are also discussed.

The F-bZIP-regulated Zn deficiency response in land plants

This review describes zinc sensing and transcriptional regulation of the zinc deficiency response in Arabidopsis, and discusses how their evolutionary conservation in land plants facilitates translational approaches for improving the Zn nutritional value of crop species. Zinc is an essential micronutrient for all living organisms due to its presence in a large number of proteins, as a structural or catalytic cofactor. In plants, zinc homeostasis mechanisms comprise uptake from soil, transport and distribution throughout the plant to provide adequate cellular zinc availability. Here, I discuss the transcriptional regulation of the response to zinc deficiency and the zinc sensing mechanisms in Arabidopsis, and their evolutionary conservation in land plants. The Arabidopsis F-group basic region leucine-zipper (F-bZIP) transcription factors bZIP19 and bZIP23 function simultaneously as sensors of intracellular zinc status, by direct binding of zinc ions, and as the central regulators of the zinc deficiency response, with their target genes including zinc transporters from the ZRT/IRT-like Protein (ZIP) family and nicotianamine synthase enzymes that produce the zinc ligand nicotianamine. I note that this relatively simple mechanism of zinc sensing and regulation, together with the evolutionary conservation of F-bZIP transcription factors across land plants, offer important research opportunities. One of them is to use the F-bZIP-regulated zinc deficiency response as a tractable module for evolutionary and comparative functional studies. Another research opportunity is translational research in crop plants, modulating F-bZIP activity as a molecular switch to enhance zinc accumulation. This should become a useful plant-based solution to alleviate effects of zinc deficiency in soils, which impact crop production and crop zinc content, with consequences for human nutrition globally.

Genome-wide association studies provide genetic insights into natural variation of seed-size-related traits in mungbean

Although mungbean (Vigna radiata (L.) R. Wilczek) is an important legume crop, its seed yield is relatively low. To address this issue, here 196 accessions with 3,607,508 SNP markers were used to identify quantitative trait nucleotides (QTNs), QTN-by-environment interactions (QEIs), and their candidate genes for seed length (SL), seed width, and 100-seed weight (HSW) in two environments. As a result, 98 QTNs and 20 QEIs were identified using 3VmrMLM, while 95, >10,000, and 15 QTNs were identified using EMMAX, GEMMA, and CMLM, respectively. Among 809 genes around these QTNs, 12 were homologous to known seed-development genes in rice and Arabidopsis thaliana, in which 10, 2, 1, and 0 genes were found, respectively, by the above four methods to be associated with the three traits, such as VrEmp24/25 for SL and VrKIX8 for HSW. Eight of the 12 genes were significantly differentially expressed between two large-seed and two small-seed accessions, and VrKIX8, VrPAT14, VrEmp24/25, VrIAR1, VrBEE3, VrSUC4, and Vrflo2 were further verified by RT-qPCR. Among 65 genes around these QEIs, VrFATB, VrGSO1, VrLACS2, and VrPAT14 were homologous to known seed-development genes in A. thaliana, although new experiments are necessary to explore these novel GEI-trait associations. In addition, 54 genes were identified in comparative genomics analysis to be associated with seed development pathway, in which VrKIX8, VrABA2, VrABI5, VrSHB1, and VrIKU2 were also identified in genome-wide association studies. This result provided a reliable approach for identifying seed-size-related genes in mungbean and a solid foundation for further molecular biology research on seed-size-related genes.

Clock-Controlled and Cold-Induced CYCLING DOF FACTOR6 Alters Growth and Development in Arabidopsis

The circadian clock represents a critical regulatory network, which allows plants to anticipate environmental changes as inputs and promote plant survival by regulating various physiological outputs. Here, we examine the function of the clock-regulated transcription factor, CYCLING DOF FACTOR 6 (CDF6), during cold stress in Arabidopsis thaliana. We found that the clock gates CDF6 transcript accumulation in the vasculature during cold stress. CDF6 mis-expression results in an altered flowering phenotype during both ambient and cold stress. A genome-wide transcriptome analysis links CDF6 to genes associated with flowering and seed germination during cold and ambient temperatures, respectively. Analysis of key floral regulators indicates that CDF6 alters flowering during cold stress by repressing photoperiodic flowering components, FLOWERING LOCUS T (FT), CONSTANS (CO), and BROTHER OF FT (BFT). Gene ontology enrichment further suggests that CDF6 regulates circadian and developmental-associated genes. These results provide insights into how the clock-controlled CDF6 modulates plant development during moderate cold stress.

Regulation of the Zinc Deficiency Response in the Legume Model Medicago truncatula

The zinc deficiency response in Arabidopsis thaliana is regulated by F-group basic region leucine-zipper (F-bZIP) transcription factors, and there is evidence of evolutionary conservation of this regulatory network in land plants. Fundamental knowledge on the zinc homeostasis regulation in crop species will contribute to improving their zinc nutritional value. Legumes are protein-rich crops, used worldwide as part of traditional diets and as animal forage, being therefore a good target for micronutrient biofortification. Here, we identified F-bZIP transcription factors in representative legume species and functionally characterized the two F-bZIPs from Medicago truncatula. Results indicate that MtFbZIP1 is the functional homolog of A. thaliana bZIP19 and bZIP23, while MtFbZIP2 does not play a role in the zinc deficiency response. Additionally, analysis of M. truncatula genes from the Zrt/Irt-like protein (ZIP) family of zinc transporters or encoding nicotianamine synthase enzymes that produce the zinc ligand nicotianamine, support the conservation of the F-bZIP-regulated zinc deficiency response in M. truncatula. Phylogenetic analysis of F-bZIP homologs enriched in legume species reinforces the branching into two groups, with MtFbZIP1 and MtFbZIP2 mapping in Groups 1 and 2, respectively. This phylogeny combined with the functional characterization of MtFbZIPs supports the suggested conservation of the zinc deficiency response associated with Group 1 F-bZIPs, and the more variable evolutionary paths associated with Group 2. Overall, we provide novel insight on the mechanisms of response to zinc deficiency in M. truncatula, which contributes to developing strategies for improving zinc content in legume crops.

Zinc transporters ZIPT-2.4 and ZIPT-15 are required for normal C. elegans fecundity

PURPOSE

The requirement of zinc for the development and maturation of germ lines and reproductive systems is deeply conserved across evolution. The nematode Caenorhabditis elegans offers a tractable platform to study the complex system of distributing zinc to the germ line. We investigated several zinc importers to investigate how zinc transporters play a role in the reproductive system in nematodes, as well as establish a platform to study zinc transporter biology in germline and reproductive development.

METHODS

Previous high throughput transcriptional datasets as well as phylogenetic analysis identified several putative zinc transporters that have a function in reproduction in worms. Phenotypic analysis of CRISPR-generated knockouts and tags included characterization of offspring output, gonad development, and protein localization. Light and immunofluorescence microscopy allowed for visualization of physiological and molecular effects of zinc transporter mutations.

RESULTS

Disruption of two zinc transporters, ZIPT-2.4 and ZIPT-15, was shown to lead to defects in reproductive output. A mutation in zipt-2.4 has subtle effects on reproduction, while a mutation in zipt-15 has a clear impact on gonad and germline development that translates into a more pronounced defect in fecundity. Both transporters have germline expression, as well as additional expression in other cell types.

CONCLUSIONS

Two ZIP-family zinc transporter orthologs of human ZIP6/10 and ZIP1/2/3 proteins are important for full reproductive fecundity and participate in development of the gonad. Notably, these zinc transporters are present in gut and reproductive tissues in addition to the germ line, consistent with a complex zinc trafficking network important for reproductive success.

Zinc in plants: Integrating homeostasis and biofortification

Zinc plays many essential roles in life. As a strong Lewis acid that lacks redox activity under environmental and cellular conditions, the Zn²⁺ cation is central in determining protein structure and catalytic function of nearly 10% of most eukaryotic proteomes. While specific functions of zinc have been elucidated at a molecular level in a number of plant proteins, wider issues abound with respect to the acquisition and distribution of zinc by plants. An important challenge is to understand how plants balance between Zn supply in soil and their own nutritional requirement for zinc, particularly where edaphic factors lead to a lack of bioavailable zinc or, conversely, an excess of zinc that bears a major risk of phytotoxicity. Plants are the ultimate source of zinc in the human diet, and human Zn deficiency accounts for over 400 000 deaths annually. Here, we review the current understanding of zinc homeostasis in plants from the molecular and physiological perspectives. We provide an overview of approaches pursued so far in Zn biofortification of crops. Finally, we outline a "push-pull" model of zinc nutrition in plants as a simplifying concept. In summary, this review discusses avenues that can potentially deliver wider benefits for both plant and human Zn nutrition.