Arabidopsis IRT2 cooperates with the high-affinity iron uptake system to maintain iron homeostasis in root epidermal cells

Nutri-cereal tissue-specific transcriptome atlas during development: Functional integration of gene expression to identify mineral uptake pathways in little millet (Panicum sumatrense)

Little millet (Panicum sumatrense Roth ex Roem. & Schult.) is an essential minor millet of southeast Asia and Africa's temperate and subtropical regions. The plant is stress-tolerant, has a short life cycle, and has a mineral-rich nutritional profile associated with unique health benefits. We report the developmental gene expression atlas of little millet (genotype JK-8) from ten tissues representing different stages of its life cycle, starting from seed germination and vegetative growth to panicle maturation. The developmental transcriptome atlas led to the identification of 342 827 transcripts. The BUSCO analysis and comparison with the transcriptomes of related species confirm that this study presents high-quality, in-depth coverage of the little millet transcriptome. In addition, the eFP browser generated here has a user-friendly interface, allowing interactive visualizations of tissue-specific gene expression. Using these data, we identified transcripts, the orthologs of which in Arabidopsis and rice are involved in nutrient acquisition, transport, and response pathways. The comparative analysis of the expression levels of these transcripts holds great potential for enhancing the mineral content in crops, particularly zinc and iron, to address the issue of "hidden hunger" and to attain nutritional security, making it a valuable asset for translational research.

Nano-enabled agrochemicals: mitigating heavy metal toxicity and enhancing crop adaptability for sustainable crop production

The primary factors that restrict agricultural productivity and jeopardize human and food safety are heavy metals (HMs), including arsenic, cadmium, lead, and aluminum, which adversely impact crop yields and quality. Plants, in their adaptability, proactively engage in a multitude of intricate processes to counteract the impacts of HM toxicity. These processes orchestrate profound transformations at biomolecular levels, showing the plant's ability to adapt and thrive in adversity. In the past few decades, HM stress tolerance in crops has been successfully addressed through a combination of traditional breeding techniques, cutting-edge genetic engineering methods, and the strategic implementation of marker-dependent breeding approaches. Given the remarkable progress achieved in this domain, it has become imperative to adopt integrated methods that mitigate potential risks and impacts arising from environmental contamination on yields, which is crucial as we endeavor to forge ahead with the establishment of enduring agricultural systems. In this manner, nanotechnology has emerged as a viable field in agricultural sciences. The potential applications are extensive, encompassing the regulation of environmental stressors like toxic metals, improving the efficiency of nutrient consumption and alleviating climate change effects. Integrating nanotechnology and nanomaterials in agrochemicals has successfully mitigated the drawbacks associated with traditional agrochemicals, including challenges like organic solvent pollution, susceptibility to photolysis, and restricted bioavailability. Numerous studies clearly show the immense potential of nanomaterials and nanofertilizers in tackling the acute crisis of HM toxicity in crop production. This review seeks to delve into using NPs as agrochemicals to effectively mitigate HM toxicity and enhance crop resilience, thereby fostering an environmentally friendly and economically viable approach toward sustainable agricultural advancement in the foreseeable future.

Differential absorption of cadmium and zinc by tobacco plants: Role of apoplastic pathway

Cadmium (Cd) contamination presents a significant challenge in global agriculture. This study explores the efficacy of chemical induction, specifically using sodium chloride (NaCl), to limit Cd uptake in tobacco (Nicotiana tabacum) and assesses its impact on essential divalent metal ions (DMIs). We conducted a comprehensive analysis encompassing ion absorption, root histology, and biochemistry to understand the influence of this method. Our results revealed that NaCl induction led to a notable 30 % decrease in Cd absorption, while maintaining minimal impact on zinc (Zn) uptake. Intriguingly, the absence of essential DMIs, such as calcium (Ca), magnesium (Mg), and Zn, was found to diminish the plant's capacity to absorb Cd. Furthermore, moderate NaCl induction resulted in an increased diameter of the root stele and enhanced lignin content, indicating a restriction of Cd absorption through the apoplastic pathway. Conversely, a compensatory absorption mechanism via the symplastic pathway appeared to be activated in the absence of essential elements. These findings highlight the potential of chemical induction as a strategy to mitigate agricultural Cd risks, offering insights into the complex interplay between plant ion transport pathways and metal uptake regulation.

IlNRAMP5 is required for cadmium accumulation and the growth in Iris lactea under cadmium exposures

Iris lactea is potentially applied for remediating Cd-contaminated soils due to the strong ability of Cd uptake and accumulation. However, its molecular mechanism underlying Cd uptake pathway remains unknown. Here, we report a member of NRAMP (Natural Resistance-Associated Macrophage Protein) family, IlNRAMP5, is involved in Cd/Mn uptake and the growth in I. lactea response to Cd. IlNRAMP5 was localized onto the plasma membrane, and was induced by Cd. It was expressed in the root cortex rather than the central vasculature, and in leaf vascular bundle and mesophyll cells. Heterologous expression in yeast showed that IlNRAMP5 could transport Cd and Mn, but not Fe. Knockdown of IlNRAMP5 triggered a significant reduction in Cd uptake, further diminishing the accumulation of Cd. In addition, silencing IlNRAMP5 disrupted Mn homeostasis by lowering Mn uptake and Mn allocation, accompanied by remarkably inhibiting photosynthesis under Cd conditions. Overall, the findings suggest that IlNRAMP5 plays versatile roles in Cd accumulation by mediating Cd uptake, and contributes to maintain the growth via modulating Mn homeostasis in I. lactea under Cd exposures. This would provide a mechanistic understanding Cd phytoremediation efficiency in planta.

Cellular clarity: a logistic regression approach to identify root epidermal regulators of iron deficiency response

BACKGROUND

Plants respond to stress through highly tuned regulatory networks. While prior works identified master regulators of iron deficiency responses in A. thaliana from whole-root data, identifying regulators that act at the cellular level is critical to a more comprehensive understanding of iron homeostasis. Within the root epidermis complex molecular mechanisms that facilitate iron reduction and uptake from the rhizosphere are known to be regulated by bHLH transcriptional regulators. However, many questions remain about the regulatory mechanisms that control these responses, and how they may integrate with developmental processes within the epidermis. Here, we use transcriptional profiling to gain insight into root epidermis-specific regulatory processes.

RESULTS

Set comparisons of differentially expressed genes (DEGs) between whole root and epidermis transcript measurements identified differences in magnitude and timing of organ-level vs. epidermis-specific responses. Utilizing a unique sampling method combined with a mutual information metric across time-lagged and non-time-lagged windows, we identified relationships between clusters of functionally relevant differentially expressed genes suggesting that developmental regulatory processes may act upstream of well-known Fe-specific responses. By integrating static data (DNA motif information) with time-series transcriptomic data and employing machine learning approaches, specifically logistic regression models with LASSO, we also identified putative motifs that served as crucial features for predicting differentially expressed genes. Twenty-eight transcription factors (TFs) known to bind to these motifs were not differentially expressed, indicating that these TFs may be regulated post-transcriptionally or post-translationally. Notably, many of these TFs also play a role in root development and general stress response.

CONCLUSIONS

This work uncovered key differences in -Fe response identified using whole root data vs. cell-specific root epidermal data. Machine learning approaches combined with additional static data identified putative regulators of -Fe response that would not have been identified solely through transcriptomic profiles and reveal how developmental and general stress responses within the epidermis may act upstream of more specialized -Fe responses for Fe uptake.

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.

Deciphering the functional roles of transporter proteins in subcellular metal transportation of plants

MAIN CONCLUSION

The role of transporters in subcellular metal transport is of great significance for plants in coping with heavy metal stress and maintaining their proper growth and development. Heavy metal toxicity is a serious long-term threat to plant growth and agricultural production, becoming a global environmental concern. Excessive heavy metal accumulation not only damages the biochemical and physiological functions of plants but also causes chronic health hazard to human beings through the food chain. To deal with heavy metal stress, plants have evolved a series of elaborate mechanisms, especially a variety of spatially distributed transporters, to strictly regulate heavy metal uptake and distribution. Deciphering the subcellular role of transporter proteins in controlling metal absorption, transport and separation is of great significance for understanding how plants cope with heavy metal stress and improving their adaptability to environmental changes. Hence, we herein introduce the detrimental effects of excessive common essential and non-essential heavy metals on plant growth, and describe the structural and functional characteristics of transporter family members, with a particular emphasis on their roles in maintaining heavy metal homeostasis in various organelles. Besides, we discuss the potential of controlling transporter gene expression by transgenic approaches in response to heavy metal stress. This review will be valuable to researchers and breeders for enhancing plant tolerance to heavy metal contamination.

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.

Brassinosteroids and gibberellic acid actively regulate the zinc detoxification mechanism of Medicago sativa L. seedlings

BACKGROUND

Zinc is one of the essential trace elements in plants. There are few studies on the phytohormone to rescue the toxicity of excessive zinc to plants. The aim of this research was to evaluate the alleviating effects of brassinosteroids (BR) and gibberellic acid (GA) on the toxicity of Medicago sativa L. (M. sativa) induced by excessive zinc.

RESULTS

After zinc, BR and GA were applied to M. sativa seedlings for 7 weeks, their physiological and biochemical properties and gene expression patterns were evaluated. BR and GA significantly weakened the inhibition effect of zinc stress on growth and biomass of M. sativa. Under zinc stress, the zinc accumulation in M. sativa roots was over 5 times that in shoots. Application of BR and GA reduced zinc accumulation in roots. The content of lipid peroxides in M. sativa decreased and the activity of antioxidant enzymes increased under BR and GA treatments. In addition, BR and GA treatment down-regulated the transcription level of MsZIP1/3/5, the transporters of zinc uptake in root cells. And BR and GA up-regulated the expressions of zinc efflux, chelation, vacuolar storage and long-distance transport related genes: MsZIP7, MsHMA1, MsZIF1, MsMTP1, MsYSL1 and MsNAS1.

CONCLUSIONS

Our findings further showed that BR and GA application to M. sativa under zinc stress can reduce zinc accumulation, promote the response of the antioxidant defense system, and actively regulate the mechanism of heavy metal detoxification. Notably, 100 nM BR performed slightly better than 100 nM GA in all aspects of the detoxification of M. sativa by excessive zinc.

Comprehensive Survey of ChIP-Seq Datasets to Identify Candidate Iron Homeostasis Genes Regulated by Chromatin Modifications

Vital biochemical reactions including photosynthesis to respiration require iron, which should be tightly regulated. Although increasing evidence reveals the importance of epigenetic regulation in gene expression and signaling, the role of histone modifications and chromatin remodeling in plant iron homeostasis is not well understood. In this study, we surveyed publicly available ChIP-seq datasets of Arabidopsis wild-type and mutants defective in key enzymes of histone modification and chromatin remodeling and compared the deposition of epigenetic marks on loci of genes involved in iron regulation. Based on the analysis, we compiled a comprehensive list of iron homeostasis genes with differential enrichment of various histone modifications. This report will provide a resource for future studies to investigate epigenetic regulatory mechanisms of iron homeostasis in plants.

The role of metal transporters in phytoremediation: A closer look at Arabidopsis

Pollution of the environment by heavy metals (HMs) has recently become a global issue, affecting the health of all living organisms. Continuous human activities (industrialization and urbanization) are the major causes of HM release into the environment. Over the years, two methods (physical and chemical) have been widely used to reduce HMs in polluted environment. However, these two methods are inefficient and very expensive to reduce the HMs released into the atmosphere. Alternatively, researchers are trying to remove the HMs by employing hyper-accumulator plants. This method, referred to phytoremediation, is highly efficient, cost-effective, and eco-friendly. Phytoremediation can be divided into five types: phytostabilization, phytodegradation, rhizofiltration, phytoextraction, and phytovolatilization, all of which contribute to HMs removal from the polluted environment. Brassicaceae family members (particularly Arabidopsis thaliana) can accumulate more HMs from the contaminated environment than those of other plants. This comprehensive review focuses on how HMs pollute the environment and discusses the phytoremediation measures required to reduce the impact of HMs on the environment. We discuss the role of metal transporters in phytoremediation with a focus on Arabidopsis. Then draw insights into the role of genome editing tools in enhancing phytoremediation efficiency. This review is expected to initiate further research to improve phytoremediation by biotechnological approaches to conserve the environment from pollution.

Multi-leveled insights into the response of the eelgrass Zostera marina L to Cu than Cd exposure

Seagrass beds are recognized as critical and among the most vulnerable habitats on the planet; seagrass colonize the coastal waters where heavy metal pollution is a serious problem. In this study, the toxic effects of copper and cadmium in the eelgrass Zostera marina L. were observed at the individual, subcellular, physiologically biochemical, and molecular levels. Both Cu and Cd stress significantly inhibited the growth and the maximal quantum yield of photosystem II (Fv/Fm); and high temperature increased the degree of heavy metal damage, while low temperatures inhibited damage. The half-effect concentration (EC₅₀) of eelgrass was 28.9 μM for Cu and 2246.8 μM for Cd, indicating Cu was much more toxic to eelgrass than Cd. The effect of Cu and Cd on photosynthesis was synergistic. After 14 days of enrichment, the concentration of Cu in leaves and roots of Z. marina was 48 and 37 times higher than that in leaf sheath, and 14 and 11 times higher than that in rhizome; and the order of Cd concentration in the organs was root > leaf > rhizome > sheath. Heavy metal uptake mainly occurred in the organelles, and Cd enrichment also occurred to a certain extent in the cytoplasm. Transcriptome results showed that a number of photosynthesis-related KEGG enrichment pathways and GO terms were significantly down-regulated under Cd stress, suggesting that the photosynthetic system of eelgrass was severely damaged at the transcriptome level, which was consistent with the significant inhibition of Fv/Fm and leaf yellowing. Under Cu stress, the genes related to glutathione metabolic pathway were significantly up-regulated, together with the increased autioxidant enzyme activity of GSH-PX. In addition, the results of recovery experiment indicated that the damage caused by short-term Cd and Cu stress under EC₅₀ was reversible. These results provide heavy metal toxic effects at multiple levels and information relating to the heavy metal resistance strategies evolved by Z. marina to absorb and isolate heavy metals, and highlight the phytoremediation potential of this species especially for Cd.

ZAT10 plays dual roles in cadmium uptake and detoxification in Arabidopsis

Cadmium (Cd) is a harmful heavy metal that is risky for plant growth and human health. The zinc-finger transcription factor ZAT10 is highly conserved with ZAT6 and ZAT12, which are involved in Cd tolerance in plants. However, the definite function of ZAT10 in Cd tolerance remains uncertain. Here, we demonstrated that ZAT10 negatively regulated Cd uptake and enhanced Cd detoxification in Arabidopsis. The expression of ZAT10 in plants is induced by Cd treatment. The zat10 mutant plants exhibited a greater sensitivity to Cd stress and accumulated more Cd in both shoot and root. Further investigations revealed that ZAT10 repressed the transcriptional activity of IRT1, which encodes a key metal transporter involved in Cd uptake. Meanwhile, ZAT10 positively regulated four heavy metal detoxification-related genes: NAS1, NAS2, IRT2, and MTP3. We further found that ZAT10 interacts with FIT, but their regulatory relationship is still unclear. In addition, ZAT10 directly bound to its own promoter and repressed its transcription as a negative feedback regulation. Collectively, our findings provided new insights into the dual functions of ZAT10 on Cd uptake and detoxification in plants and pointed to ZAT10 as a potential gene resource for Cd tolerance improvement in plants.

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.

Mediation of Zinc and Iron Accumulation in Maize by ZmIRT2, a Novel Iron-Regulated Transporter

Iron (Fe) is an essential micronutrient for plant growth. Iron-regulated transporters (IRTs) play important roles in Fe2+ uptake and transport in strategy I plants. Maize (Zea mays) belongs to a strategy II plant, in which mugineic acid (MA)-Fe3+ uptake is mainly carried out by Yellow Stripe 1 (YS1). However, ZmIRT1 was previously identified by our laboratory. In this study, we isolated a novel gene from maize (ZmIRT2), which is highly homologous to OsIRT2 and ZmIRT1. ZmIRT2 was expressed in roots and anther and was induced by Fe and zinc (Zn) deficiencies. ZmIRT2-GFP fusion protein localized to the plasma membrane and endoplasmic reticulum. ZmIRT2 reversed growth defects involving Zn and Fe uptake in mutant yeast. ZmIRT2 overexpression in maize led to elevated Zn and Fe levels in roots, shoots and seeds of transgenic plants. Transcript levels of ZmIRT1 were elevated in roots, while levels of YS1 were reduced in shoots of ZmIRT2 transgenic plants. Our results imply that ZmIRT2 may function solely with ZmIRT1 to mediate Fe uptake in roots. ZmIRT1, ZmIRT2 and ZmYS1 may function in a cooperative manner to maintain Zn and Fe homeostasis in ZmIRT2 overexpressing plants. Furthermore, ZmIRT2 could be used in fortification efforts to elevate Zn and Fe levels in crop plants.

Genome-Wide Identification and Expression Profile Reveal Potential Roles of Peanut ZIP Family Genes in Zinc/Iron-Deficiency Tolerance

Zinc/iron-regulated transporter-like protein (ZIP) family genes play crucial roles in metal uptake and transport in plants. However, little is known about their functions in peanut. Here, genome-wide analysis identified 30 peanut AhZIP genes that were divided into four classes. Most AhZIPs experienced whole-genome or segmental duplication. AhZIP proteins harbored 3–8 transmembrane domains and a typical ZIP domain, showing considerable homology with BbZIP from Bordetella bronchiseptica. Clustered AhZIPs generally share similar gene/protein structures; however, unique features were found in AhIRT1.2, AhZIP1.2, AhZIP3.5 and AhZIP7.8. RNA-seq data revealed that AhZIP2.1/2.2, AhZIP4.1/4.2 and AhZIP11.1/11.2 were highly and preferentially expressed in roots, nodule and reproductive tissues. RT-qPCR analysis indicated that transcriptional responses of AhZIPs to Fe/Zn deficiency are cultivar dependent. The expressions of AhIRT1.1, AhIRT1.2 and AhZIP6.1 were closely related to Fe uptake and translocation. AhIRT1.1 and AhZIP7.2 expression were significantly correlated with Zn accumulation. The expression of AhIRT1.1, AhIRT1.2, AhZIP3.6, AhZIP6.1 and AhZIP11.1 was associated with Mn uptake and translocation. The results confirmed that AhZIP genes play crucial roles in the uptake and transport of Fe, Zn and Mn in peanut, providing clues to further functionally characterize AhZIP genes in the future.

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.

Recent advances in physiological and molecular mechanisms of heavy metal accumulation in plants

Among abiotic stress, the toxicity of metals impacts negatively on plants' growth and productivity. This toxicity promotes various perturbations in plants at different levels. To withstand stress, plants involve efficient mechanisms through the implication of various signaling pathways. These pathways enhance the expression of many target genes among them gene coding for metal transporters. Various metal transporters which are localized at the plasma membrane and/or at the tonoplast are crucial in metal stress response. Furthermore, metal detoxification is provided by metal-binding proteins like phytochelatins and metallothioneins. The understanding of the molecular basis of metal toxicities signaling pathways and tolerance mechanisms is crucial for genetic engineering to produce transgenic plants that enhance phytoremediation. This review presents an overview of the recent advances in our understanding of metal stress response. Firstly, we described the effect of metal stress on plants. Then, we highlight the mechanisms involved in metal detoxification and the importance of the regulation in the response to heavy metal stress. Finally, we mentioned the importance of genetic engineering for enhancing the phytoremediation technique. In the end, the response to heavy metal stress is complex and implicates various components. Thus, further studies are needed to better understand the mechanisms involved in response to this abiotic stress.

TpIRT1 from Polish wheat (Triticum polonicum L.) enhances the accumulation of Fe, Mn, Co, and Cd in Arabidopsis

Uptake and internal transport of micronutrients are essential for plant growth, development, and yield. In this regard, Iron Regulated Transporters (IRTs) from the Zinc Regulated Transporter (ZRT)/IRT-related protein (ZIP) family play an important role in transition metal uptake. Most studies have been focused on IRT1-like proteins in diploid species. Information on IRT1-like proteins in polyploids is limited. Here, we studied the function of TpIRT1A and TpIRT1B homoeologs in a tetraploid crop, Polish wheat (Triticum polonicum L.). Our results highlighted the importance of TpIRT1 in mediating the uptake and translocation of Fe, Mn, Co, and Cd with direct implications for wheat yield potential. Both TpIRT1A and TpIRT1B were located at the plasma membrane and internal vesicle-like organelle in protoplasts of Arabidopsis thaliana L. and increased Cd and Co sensitivity in yeast. The over-expression of TpIRT1B in A. thaliana increased Fe, Mn, Co, and Cd concentration in its tissues and improved plant growth under Fe, Mn, and Co deficiencies, while increased the sensitivity to Cd compared to wild type. Functional analysis of IRT1 homoeologs from tetraploid and diploid ancestral wheat species in yeast disclosed four distinct amino acid residues in TdiIRT1B (T. dicoccum L. (Schrank)) and TtuIRT1B (T. turgidum L.). Together, our results increase the knowledge of IRT1 function in a globally important crop, wheat.

Differences in mineral accumulation and gene expression profiles between two metal hyperaccumulators, Noccaea japonica and Noccaea caerulescens ecotype Ganges, under excess nickel condition

Here we compare mineral accumulation and global gene expression patterns between two metal hyperaccumulator plants - Noccaea japonica, originating from Ni-rich serpentine soils, and Noccaea caerulescens (ecotype Ganges), originating from Zn/Pb-mine soils - under excess Ni conditions. Significant differences in the accumulation of K, P, Mg, B, and Mo were explained by the expression levels of specific transporters for each mineral. We previously showed that total Ni accumulation in the whole plant is higher in N. caerulescens than in N. japonica. Here we found a similar tendency for Fe under excess Ni; however, the expression of iron-regulated transporter 1 (IRT1), which encodes the primary Fe uptake transporter and causes excess Ni uptake in Arabidopsis thaliana, was higher in N. japonica. NjIRT1 has a point mutation at Asp100, which is essential for Fe transport, and so might lack its Fe and possibly Ni transport function. Noccaea japonica might have lost its IRT1 function, which would prevent excess Ni uptake via IRT1 in Ni-rich soils, and come to rely on other transporters.

Metal transporters in organelles and their roles in heavy metal transportation and sequestration mechanisms in plants

Heavy metal toxicity is one of the major concerns for agriculture and health. Accumulation of toxic heavy metals at high concentrations in edible parts of crop plants is the primary cause of disease in humans and cattle. A dramatic increase in industrialization, urbanization, and other high anthropogenic activities has led to the accumulation of heavy metals in agricultural soil, which has consequently disrupted soil conditions and affected crop yield. By now, plants have developed several mechanisms to cope with heavy metal stress. However, not all plants are equally effective in dealing with the toxicity of high heavy metal concentrations. Plants have modified their anatomy, morphophysiology, and molecular networks to survive under changing environmental conditions. Heavy metal sequestration is one of the essential processes evolved by some plants to deal with heavy metals' toxic concentration. Some plants even have the ability to accumulate metals in high quantities in the shoots/organelles without toxic effects. For intercellular and interorganeller metal transport, plants harbor spatially distributed various transporters which mainly help in uptake, translocation, and redistribution of metals. This review discusses different heavy metal transporters in different organelles and their roles in metal sequestration and redistribution to help plants cope with heavy metal stress. A good understanding of the processes at stake helps in developing more tolerant crops without affecting their productivity.

High-resolution genome-wide association study pinpoints metal transporter and chelator genes involved in the genetic control of element levels in maize grain

Despite its importance to plant function and human health, the genetics underpinning element levels in maize grain remain largely unknown. Through a genome-wide association study in the maize Ames panel of nearly 2,000 inbred lines that was imputed with ∼7.7 million SNP markers, we investigated the genetic basis of natural variation for the concentration of 11 elements in grain. Novel associations were detected for the metal transporter genes rte2 (rotten ear2) and irt1 (iron-regulated transporter1) with boron and nickel, respectively. We also further resolved loci that were previously found to be associated with one or more of five elements (copper, iron, manganese, molybdenum, and/or zinc), with two metal chelator and five metal transporter candidate causal genes identified. The nas5 (nicotianamine synthase5) gene involved in the synthesis of nicotianamine, a metal chelator, was found associated with both zinc and iron and suggests a common genetic basis controlling the accumulation of these two metals in the grain. Furthermore, moderate predictive abilities were obtained for the 11 elemental grain phenotypes with two whole-genome prediction models: Bayesian Ridge Regression (0.33–0.51) and BayesB (0.33–0.53). Of the two models, BayesB, with its greater emphasis on large-effect loci, showed ∼4–10% higher predictive abilities for nickel, molybdenum, and copper. Altogether, our findings contribute to an improved genotype-phenotype map for grain element accumulation in maize.

Cadmium Accumulation Involves Synthesis of Glutathione and Phytochelatins, and Activation of CDPK, CaMK, CBLPK, and MAPK Signaling Pathways in Ulva compressa

In order to analyze the effect of cadmium in Ulva compressa (Chlorophyta), the alga was cultivated with 10, 25, and 50 μM of cadmium for 7 days, and the level of intracellular cadmium was determined. Intracellular cadmium showed an increase on day 1, no change until day 5, and an increase on day 7. Then, the alga was cultivated with 10 μM for 7 days, and the level of hydrogen peroxide, superoxide anions, and lipoperoxides; activities of antioxidant enzymes ascorbate peroxidase (AP), dehydroascorbate reductase (DHAR), and glutathione reductase (GR); the level of glutathione (GSH) and ascorbate (ASC); and the level of phytochelatins (PCs) and transcripts encoding metallothioneins (UcMTs) levels were determined. The level of hydrogen peroxide increased at 2 and 12 h, superoxide anions on day 1, and lipoperoxides on days 3 to 5. The activities of AP and GR were increased, but not the DHAR activity. The level of GSH increased on day 1, decreased on day 3, and increased again on day 5, whereas ASC slightly increased on days 3 and 7, and activities of enzymes involved in GSH and ASC synthesis were increased on days 3 to 7. The level of PC2 and PC4 decreased on day 3 but increased again on day 5. The level of transcripts encoding UcMT1 and UcMT2 increased on days 3 to 5, mainly that of UcMT2. Thus, cadmium accumulation induced an oxidative stress condition that was mitigated by the activation of antioxidant enzymes and synthesis of GSH and ASC. Then, the alga cultivated with inhibitors of calcium-dependent protein kinases (CDPKs), calmodulin-dependent protein kinases (CaMKs), calcineurin B-like protein kinases (CBLPKs), and MAPKs and 10 μM of cadmium for 5 days showed a decrease in intracellular cadmium and in the level of GSH and PCs, with the four inhibitors, and in the level of transcripts encoding UcMTs, with two inhibitors. Thus, CDPKs, CaMK, CBLPKS, and MAPKs are involved in cadmium accumulation and GSH and PC synthesis, and GSH and PCs and/or UcMTs may participate in cadmium accumulation.

Breeding for low cadmium accumulation cereals

Cadmium (Cd) is an element that is nonessential and extremely toxic to both plants and human beings. Soil contaminated with Cd has adverse impacts on crop yields and threatens human health via the food chain. Cultivation of low-Cd cultivars has been of particular interest and is one of the most cost-effective and promising approaches to minimize human dietary intake of Cd. Low-Cd crop cultivars should meet particular criteria, including acceptable yield and quality, and their edible parts should have Cd concentrations below maximum permissible concentrations for safe consumption, even when grown in Cd-contaminated soil. Several low-Cd cereal cultivars and genotypes have been developed worldwide through cultivar screening and conventional breeding. Molecular markers are powerful in facilitating the selection of low-Cd cereal cultivars. Modern molecular breeding technologies may have great potential in breeding programs for the development of low-Cd cultivars, especially when coupled with conventional breeding. In this review, we provide a synthesis of low-Cd cereal breeding.

Coordinated homeostasis of essential mineral nutrients: a focus on iron

In plants, iron (Fe) transport and homeostasis are highly regulated processes. Fe deficiency or excess dramatically limits plant and algal productivity. Interestingly, complex and unexpected interconnections between Fe and various macro- and micronutrient homeostatic networks, supposedly maintaining general ionic equilibrium and balanced nutrition, are currently being uncovered. Although these interactions have profound consequences for our understanding of Fe homeostasis and its regulation, their molecular bases and biological significance remain poorly understood. Here, we review recent knowledge gained on how Fe interacts with micronutrient (e.g. zinc, manganese) and macronutrient (e.g. sulfur, phosphate) homeostasis, and on how these interactions affect Fe uptake and trafficking. Finally, we highlight the importance of developing an improved model of how Fe signaling pathways are integrated into functional networks to control plant growth and development in response to fluctuating environments.

Cadmium toxicity in plants: Impacts and remediation strategies

Cadmium (Cd) is an unessential trace element in plants that is ubiquitous in the environment. Anthropogenic activities such as disposal of urban refuse, smelting, mining, metal manufacturing, and application of synthetic phosphate fertilizers enhance the concentration of Cd in the environment and are carcinogenic to human health. In this manuscript, we reviewed the sources of Cd contamination to the environment, soil factors affecting the Cd uptake, the dynamics of Cd in the soil rhizosphere, uptake mechanisms, translocation, and toxicity of Cd in plants. In crop plants, the toxicity of Cd reduces uptake and translocation of nutrients and water, increases oxidative damage, disrupts plant metabolism, and inhibits plant morphology and physiology. In addition, the defense mechanism in plants against Cd toxicity and potential remediation strategies, including the use of biochar, minerals nutrients, compost, organic manure, growth regulators, and hormones, and application of phytoremediation, bioremediation, and chemical methods are also highlighted in this review. This manuscript may help to determine the ecological importance of Cd stress in interdisciplinary studies and essential remediation strategies to overcome the contamination of Cd in agricultural soils.

Importance of the Rhizosphere Microbiota in Iron Biofortification of Plants

Increasing the iron content of plant products and iron assimilability represents a major issue for human nutrition and health. This is also a major challenge because iron is not readily available for plants in most cultivated soils despite its abundance in the Earth's crust. Iron biofortification is defined as the enhancement of the iron content in edible parts of plants. This biofortification aims to reach the objectives defined by world organizations for human nutrition and health while being environment friendly. A series of options has been proposed to enhance plant iron uptake and fight against hidden hunger, but they all show limitations. The present review addresses the potential of soil microorganisms to promote plant iron nutrition. Increasing knowledge on the plant microbiota and plant-microbe interactions related to the iron dynamics has highlighted a considerable contribution of microorganisms to plant iron uptake and homeostasis. The present overview of the state of the art sheds light on plant iron uptake and homeostasis, and on the contribution of plant-microorganism (plant-microbe and plant-plant-microbe) interactions to plant nutritition. It highlights the effects of microorganisms on the plant iron status and on the co-occurring mechanisms, and shows how this knowledge may be valued through genetic and agronomic approaches. We propose a change of paradigm based on a more holistic approach gathering plant and microbial traits mediating iron uptake. Then, we present the possible applications in plant breeding, based on plant traits mediating plant-microbe interactions involved in plant iron uptake and physiology.

Reduced cadmium accumulation in tobacco by sodium chloride priming

Cadmium (Cd) pollution threatens agricultural security worldwide. This study tested the efficacy of priming chemicals to decrease Cd uptake by tobacco plants (Nicotiana tabacum). After initial screening from nine different chemicals (NaCl, Cd(CH3COO)2, Cd(NO3)2, CdCl2, KHNO3, polyethylene glycol 6000 (PEG-6000), indole-3-acetic acid (IAA), ß-aminobutyric acid (BABA), and glutathione (GSH)), NaCl and PEG-6000 were further investigated because of their low risks to plant growth and efficiency to Cd reduction. Priming procedures (concentrations) were optimized for both chemicals and the best one (100 mM NaCl) was used to test both soil and hydroponic media. The results showed 31.3% lower Cd concentrations in shoots after priming with 100 mM NaCl. Phenotype parameters of the plants were also measured and showed no significant impacts of the priming procedures on the shoot biomass and the uptakes of nitrogen (N), phosphorus (P), and potassium (K), nor the photosynthetic capacity (net photosynthesis rate (Pn) and chlorophyll concentration (SPAD)). Histological observations of the roots showed a significant increase of the stele diameter after NaCl priming and a subsequent negative correlation between shoot Cd concentration and stele diameter was found after NaCl priming at different levels. This study confirmed 100 mM NaCl as an efficient priming treatment to decrease Cd uptake and the coarsening of the root stele was identified as a potential explanation for the observed decrease of Cd in tobacco shoots.

Cadmium in plants: uptake, toxicity, and its interactions with selenium fertilizers

Cd is the third major contaminant of greatest hazard to the environment after mercury and lead and is considered as the only metal that poses health risks to both humans and animals at plant tissue concentrations that are generally not phytotoxic. Cd accumulation in plant shoots depends on Cd entry through the roots, sequestration within root vacuoles, translocation in the xylem and phloem, and Cd dilution within the plant shoot throughout its growth. Several metal transporters, processes, and channels are involved from the first step of Cd reaching the root cells and until its final accumulation in the edible parts of the plant. It is hard to demonstrate one step as the pivotal factor to decide the Cd tolerance or accumulation ability of plants since the role of a specific transporter/process varies among plant species and even cultivars. In this review, we discuss the sources of Cd pollutants, Cd toxicity to plants, and mechanisms of Cd uptake and redistribution in plant tissues. The metal transporters involved in Cd transport within plant tissues are also discussed and how their manipulation can control Cd uptake and/or translocation. Finally, we discuss the beneficial effects of Se on plants under Cd stress, and how it can minimize or mitigate Cd toxicity in plants.

Oryza sativa FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (OsFIT/OsbHLH156) interacts with OsIRO2 to regulate iron homeostasis

Iron (Fe) is indispensable for the growth and development of plants. It is well known that FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) is a key regulator of Fe uptake in Arabidopsis. Here, we identify the Oryza sativa FIT (also known as OsbHLH156) as the interacting partner of IRON-RELATED BHLH TRANSCRIPTION FACTOR 2 (OsIRO2) that is critical for regulating Fe uptake. The OsIRO2 protein is localized in the cytoplasm and nucleus, but OsFIT facilitates the accumulation of OsIRO2 in the nucleus. Loss-of-function mutations of OsFIT result in decreased Fe accumulation, severe Fe-deficiency symptoms, and disrupted expression of Fe-uptake genes. In contrast, OsFIT overexpression promotes Fe accumulation and the expression of Fe-uptake genes. Genetic analyses indicate that OsFIT and OsIRO2 function in the same genetic node. Further analyses suggest that OsFIT and OsIRO2 form a functional transcription activation complex to initiate the expression of Fe-uptake genes. Our findings provide a mechanism understanding of how rice maintains Fe homeostasis.

Endomembrane Reorganization Induced by Heavy Metals

Plant cells maintain plasmatic concentrations of essential heavy metal ions, such as iron, zinc, and copper, within the optimal functional range. To do so, several molecular mechanisms have to be committed to maintain concentrations of non-essential heavy metals and metalloids, such as cadmium, mercury and arsenic below their toxicity threshold levels. Compartmentalization is central to heavy metals homeostasis and secretory compartments, finely interconnected by traffic mechanisms, are determinant. Endomembrane reorganization can have unexpected effects on heavy metals tolerance altering in a complex way membrane permeability, storage, and detoxification ability beyond gene's expression regulation. The full understanding of endomembrane role is propaedeutic to the comprehension of translocation and hyper-accumulation mechanisms and their applicative employment. It is evident that further studies on dynamic localization of these and many more proteins may significantly contribute to the understanding of heavy metals tolerance mechanisms. The aim of this review is to provide an overview about the endomembrane alterations involved in heavy metals compartmentalization and tolerance in plants.

FIT, a regulatory hub for iron deficiency and stress signaling in roots, and FIT-dependent and -independent gene signatures

Iron (Fe) is vital for plant growth. Plants balance the beneficial and toxic effects of this micronutrient, and tightly control Fe uptake and allocation. Here, we review the role of the basic helix-loop-helix (bHLH) transcription factor FIT (FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) in Fe acquisition. FIT is not only essential, it is also a central regulatory hub in root cells to steer and adjust the rate of Fe uptake by the root in a changing environment. FIT regulates a subset of root Fe deficiency (-Fe) response genes. Based on a combination of co-expression network and FIT-dependent transcriptome analyses, we defined a set of FIT-dependent and FIT-independent gene expression signatures and co-expression clusters that encode specific functions in Fe regulation and Fe homeostasis. These gene signatures serve as markers to integrate novel regulatory factors and signals into the -Fe response cascade. FIT forms a complex with bHLH subgroup Ib transcription factors. Furthermore, it interacts with key regulators from different signaling pathways that either activate or inhibit FIT function to adjust Fe acquisition to growth and environmental constraints. Co-expression clusters and FIT protein interactions suggest a connection of -Fe with ABA responses and root cell elongation processes that can be explored in future studies.

Early Responses of Brassica oleracea Roots to Zinc Supply Under Sufficient and Sub-Optimal Phosphorus Supply

Shoot zinc (Zn) concentration in Brassica oleracea is affected by soil Zn and phosphorus (P) supply. Most problematic is the negative impact of P fertilizers on Zn concentrations in crops, which makes balancing yield and mineral quality challenging. To evaluate early molecular mechanisms involved in the accumulation of large shoot Zn concentrations regardless of the P supply, two B. oleracea accessions differing in root architecture and root exudates were grown hydroponically for two weeks with different combinations of P and Zn supply. Ionome profiling and deep RNA sequencing of roots revealed interactions of P and Zn in planta, without apparent phenotypic effects. In addition, increasing P supply did not reduce tissue Zn concentration. Substantial changes in gene expression in response to different P and/or Zn supplies in roots of both accessions ensured nutritionally sufficient P and Zn uptake. Numerous genes were differentially expressed after changing Zn or P supply and most of them were unique to only one accession, highlighting their different strategies in achieving nutrient sufficiency. Thus, different gene networks responded to the changing P and Zn supply in the two accessions. Additionally, enrichment analysis of gene ontology classes revealed that genes involved in lipid metabolism, response to starvation, and anion transport mechanisms were most responsive to differences in P and Zn supply in both accessions. The results agreed with previously studies demonstrating alterations in P and Zn transport and phospholipid metabolism in response to reduced P and Zn supply. It is anticipated that improved knowledge of genes responsive to P or Zn supply will help illuminate the roles in uptake and accumulation of P and Zn and might identify candidate genes for breeding high-yield-high-Zn brassicas.

OsZIP1 functions as a metal efflux transporter limiting excess zinc, copper and cadmium accumulation in rice

BACKGROUND

Metal homeostasis is critical for plant growth, development and adaptation to environmental stresses and largely governed by a variety of metal transporters. The plant ZIP (Zn-regulated transporter, Iron-regulated transporter-like Protein) family proteins belong to the integral membrane transporters responsible for uptake and allocation of essential and non-essential metals. However, whether the ZIP family members mediate metal efflux and its regulatory mechanism remains unknown.

RESULTS

In this report, we provided evidence that OsZIP1 is a metal-detoxified transporter through preventing excess Zn, Cu and Cd accumulation in rice. OsZIP1 is abundantly expressed in roots throughout the life span and sufficiently induced by excess Zn, Cu and Cd but not by Mn and Fe at transcriptional and translational levels. Expression of OsZIP-GFP fusion in rice protoplasts and tobacco leaves shows that OsZIP1 resides in the endoplasmic reticulum (ER) and plasma membrane (PM). The yeast (Saccharomyces cerevisiae) complementation test shows that expression of OsZIP1 reduced Zn accumulation. Transgenic rice overexpressing OsZIP1 grew better under excess metal stress but accumulated less of the metals in plants. In contrast, both oszip1 mutant and RNA interference (RNAi) lines accumulated more metal in roots and contributed to metal sensitive phenotypes. These results suggest OsZIP1 is able to function as a metal exporter in rice when Zn, Cu and Cd are excess in environment. We further identified the DNA methylation of histone H3K9me2 of OsZIP1 and found that OsZIP1 locus, whose transcribed regions imbed a 242 bp sequence, is demethylated, suggesting that epigenetic modification is likely associated with OsZIP1 function under Cd stress.

CONCLUSION

OsZIP1 is a transporter that is required for detoxification of excess Zn, Cu and Cd in rice.

Cadmium and/or copper excess induce interdependent metal accumulation, DNA methylation, induction of metal chelators and antioxidant defences in the seagrass Zostera marina

In this investigation, we assessed the effects of Cu and/or Cd excess on physiological and metabolic processes of the widespread seagrass Zostera marina. Adult were exposed to low Cd and Cu (0.89 and 0.8 μM, respectively) and high Cd and Cu (8.9 and 2.4 μM, respectively) for 6 d at: Control conditions; low Cu; high Cu; low Cd; high Cd; low Cd and low Cu; and high Cd and high Cu. Photosynthetic performance decreased under single and combined treatments, although effects were more negative under Cu than Cd. Total Cu accumulation was higher than Cd, under single and combined treatments; however, their accumulation was generally lower when applied together, suggesting competition among them. Levels of glutathione (GSH) and phytochelatins (PCs) followed patterns similar to metal accumulation, with up to PC5, displaying adaptations in tolerance. A metallothionein (MET) gene showed upregulation only at high Cd, low Cu, and high Cu. The expression of the enzymes glutathione reductase (GR), ascorbate peroxidase (APX), and catalase (CAT) was greatest at high Cu, and at high Cd and Cu together; the highest expression was under Cu, alone and combined. Both metals induced upregulation of the DNA methyltransferases CMT3 and DRM2, with the highest expression at single Cu. The DNA demethylation ROS1 was overexpressed in treatments containing high Cu, suggesting epigenetic modifications. The results show that under copper and/or cadmium, Z. marina was still biologically viable; certainly based, at least in part, on the induction of metal chelators, antioxidant defences and methylation/demethylation pathways of gene regulation.

Maize factors ZmUBP15, ZmUBP16 and ZmUBP19 play important roles for plants to tolerance the cadmium stress and salt stress

Ubiquitin-Specific Protease16 (UBP16) has been described involved in cadmium stress and salt stress in Arabidopsis, however nothing is known about the functions of its homologs in maize. In this study, we investigate the functions of ZmUBP15, ZmUBP16 and ZmUBP19, three Arabidopsis UBP16 homologs in maize. Our results indicate that ZmUBP15, ZmUBP16 and ZmUBP19 are ubiquitously expressed throughout plant development, and ZmUBP15, ZmUBP16 and ZmUBP19 proteins are mainly localized in plasma membrane. Complementation analyses show that over-expression of ZmUBP15 or ZmUBP16 can rescue the defective phenotype of ubp16-1 in cadmium stress. In addition, over-expression of ZmUBP15, ZmUBP16 or ZmUBP19 can increase the plant tolerance to cadmium stress. These results indicate that ZmUBP15, ZmUBP16 and ZmUBP19 are required for plant to tolerance the cadmium stress. Consistent with this point, cadmium-related genes are markedly up-regulated in seedlings over-expressing ZmUBP15, ZmUBP16 or ZmUBP19. Furthermore, our data indicate that ZmUBP15, ZmUBP16 and ZmUBP19 partially rescue the salt-stress phenotype of ubp16-1. Thus, our research uncover the functions of three novel maize proteins, ZmUBP15, ZmUBP16 and ZmUBP19, which are required for plants in response to cadmium stress and salt stress.

Arabidopsis and rice showed a distinct pattern in ZIPs genes expression profile in response to Cd stress

BACKGROUND

Plant ZIP genes represent an important transporter family involved in metal transport. Evidence has implied that some ZIPs may contribute to plant Cd uptake, but a genome-wide examination of ZIPs' role in Cd tolerance and uptake has rarely been reported. In this study, a genome-wide bioinformatic screening of candidate ZIP genes in Arabidopsis and rice was performed, followed by a systematic determination of their expression profile in response to Cd stress. Typical up-regulated ZIPs genes were then expressed in yeast cells to examine their effect on hosts' Cd uptake.

RESULTS

A total of 27 ZIP genes in Arabidopsis and rice were screened out based on sequence similarity. In Arabidopsis, Cd exposure strongly impacted the expression of most ZIPs, among which AtIRT1, AtIRT2, AtIRT4 AtZIP9, AtZIP10 and AtZIP12 were sharply up-regulated and AtIRT3, AtIRT5 were significantly down-regulated in root. In rice, all tested genes in shoot except for OsIRT1 and OsIRT12 were sharply up-regulated, while OsIRT1 and OsZIP1 in root were significantly down-regulated. Interestingly, some genes like AtIRT3, AtZIP5, AtZIP12, OsIRT1 and OsZIP1 showed converse expression regulation when subject to the tested Cd stress. When expressed in yeast cells, three ZIPs, AtIRT1, OsZIP1 and OsZIP3, caused a substantial increase in Cd sensitivity and Cd accumulation of the host cells.

CONCLUSIONS

In conclusion, this study revealed a distinct pattern in ZIPs family genes expression between Arabidopsis and rice in response to Cd stress. Arabidopsis mainly up-regulated root ZIPs genes, while rice mainly up-regulated shoot ZIPs genes. Three genes, AtIRT1, OsZIP1 and OsZIP3, conferred an increased Cd accumulation and sensitivity to Cd stress when expressed in yeast cells, further implying their roles in Cd uptake in plants.

Comparative RNA-seq analysis of nickel hyperaccumulating and non-accumulating populations of Senecio coronatus (Asteraceae)

Most metal hyperaccumulating plants accumulate nickel, yet the molecular basis of Ni hyperaccumulation is not well understood. We chose Senecio coronatus to investigate this phenomenon as this species displays marked variation in shoot Ni content across ultramafic outcrops in the Barberton Greenstone Belt (South Africa), thus allowing an intraspecific comparative approach to be employed. No correlation between soil and shoot Ni contents was observed, suggesting that this variation has a genetic rather than environmental basis. This was confirmed by our observation that the accumulation phenotype of plants from two hyperaccumulator and two non-accumulator populations was maintained when the plants were grown on a soil mix from these four sites for 12 months. We analysed the genetic variation among 12 serpentine populations of S. coronatus, and used RNA-seq for de novo transcriptome assembly and analysis of gene expression in hyperaccumulator versus non-accumulator populations. Genetic analysis revealed the presence of hyperaccumulators in two well supported evolutionary lineages, indicating that Ni hyperaccumulation may have evolved more than once in this species. RNA-Seq analysis indicated that putative homologues of transporters associated with root iron uptake in plants are expressed at elevated levels in roots and shoots of hyperaccumulating populations of S. coronatus from both evolutionary lineages. We hypothesise that Ni hyperaccumulation in S. coronatus may have evolved through recruitment of these transporters, which play a role in the iron-deficiency response in other plant species.

Adaptation to high zinc depends on distinct mechanisms in metallicolous populations of Arabidopsis halleri

Zinc (Zn) hyperaccumulation and hypertolerance are highly variable traits in Arabidopsis halleri. Metallicolous populations have evolved from nearby nonmetallicolous populations in multiple independent adaptation events. To determine whether these events resulted in similar or divergent adaptive strategies to high soil Zn concentrations, we compared two A. halleri metallicolous populations from distant genetic units in Europe (Poland (PL22) and Italy (I16)). The ionomic (Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES)) and transcriptomic (RNA sequencing (RNA-Seq)) responses to growth at 5 and 150 μM Zn were analyzed in root and shoot tissues to examine the contribution of the geographic origin and treatment to variation among populations. These analyses were enabled by the generation of a reference A. halleri transcriptome assembly. The genetic unit accounted for the largest variation in the gene expression profile, whereas the two populations had contrasting Zn accumulation phenotypes and shared little common response to the Zn treatment. The PL22 population displayed an iron deficiency response at high Zn in roots and shoots, which may account for higher Zn accumulation. By contrast, I16, originating from a highly Zn-contaminated soil, strongly responded to control conditions. Our data suggest that distinct mechanisms support adaptation to high Zn in soils among A. halleri metallicolous populations.

GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis

How plants determine the final size of growing cells is an important, yet unresolved, issue. Root hairs provide an excellent model system with which to study this as their final cell size is remarkably constant under constant environmental conditions. Previous studies have demonstrated that a basic helix-loop helix transcription factor ROOT HAIR DEFECTIVE 6-LIKE 4 (RSL4) promotes root hair growth, but how hair growth is terminated is not known. In this study, we demonstrate that a trihelix transcription factor GT-2-LIKE1 (GTL1) and its homolog DF1 repress root hair growth in Arabidopsis. Our transcriptional data, combined with genome-wide chromatin-binding data, show that GTL1 and DF1 directly bind the RSL4 promoter and regulate its expression to repress root hair growth. Our data further show that GTL1 and RSL4 regulate each other, as well as a set of common downstream genes, many of which have previously been implicated in root hair growth. This study therefore uncovers a core regulatory module that fine-tunes the extent of root hair growth by the orchestrated actions of opposing transcription factors.

Summary:Arabidopsis gtl1 df1 double mutants and tissue-specific overexpression of GTL1 and DF1 demonstrate that both GTL1 and DF1 negatively regulate root hair growth by directly repressing RSL4.

Tracing the role of plant proteins in the response to metal toxicity: a comprehensive review

Plants are sessile in nature, but are capable to evade from high level concentration of heavy metals like Cd, Hg, Cu, through various metabolic pathways. Some of the pathways regulate normal metabolism in plants, whereas others are required for for their survival under metal toxicity. Different plant proteins act as transporters to transfer metal from one organelle to the other and further eliminate it out from the plants. Initially, exposure of heavy metals/metalloids to plants lead to over expression of proteins which in turn stimulate other stress-related genes. Further, they activate signalling mechanism like MAPK cascade, Cd-Calmodulin signalling pathway, and oxidation signalling pathway that lead to generation of ROS (reactive oxygen species). Once these ROS (highly unstable) are formed, they generate free radicals which react with macromolecules like proteins and DNA. This has negative impact on plant growth and leads to ageing and, eventually, cell death. The uncontrolled, destructive processes damage plants physiologically and ultimately lead to oxidative stress. Activation of antioxidant enzymes like SOD (superoxide dismutase) and CAT (catalase) allows plants to cope under oxidative stress conditions. Among plant proteins, some of the antioxidant enzymes like glutathione, and APX (ascorbate peroxidase) play defensive roles against abiotic stress in plants. Chaperones help in protein folding to maintain protein stability under stress conditions. With this background, the present review gives a brief account of the functions, localization and expression pattern of plant proteins against metal/metalloid toxicity. Moreover, the aim of this review is also to summarize the cutting edge research of plant protein and metal interfaces and their future prospects.

Rootstock influence on iron uptake responses in Citrus leaves and their regulation under the Fe paradox effect

BACKGROUND AND AIMS

This work evaluates the regulation of iron uptake responses in Citrus leaves and their involvement in the Fe paradox effect.

METHODS

Experiments were performed in field-grown 'Navelina' trees grafted onto two Cleopatra mandarin × Poncirus trifoliata (L.) Raf. hybrids with different Fe-chlorosis symptoms: 030146 (non-chlorotic) and 030122 (chlorotic).

RESULTS

Chlorotic leaves were smaller than non-chlorotic ones for both dry weight (DW) and area basis, and exhibited marked photosynthetic state affection, but reduced catalase and peroxidase enzymatic activities. Although both samples had a similar total Fe concentration on DW, it was lower in chlorotic leaves when expressed on an area basis. A similar pattern was observed for the total Fe concentration in the apoplast and cell sap and in active Fe (Fe2+) concentration. FRO2 gene expression and ferric chelate reductase (FC-R) activity were also lower in chlorotic samples, while HA1 and IRT1 were more induced. Despite similar apoplasmic pH, K+/Ca2+ was higher in chlorotic leaves, and both citrate and malate concentrations in total tissue and apoplast fluid were lower.

CONCLUSION

(1) The rootstock influences Fe acquisition system in the leaf; (2) the increased sensitivity to Fe-deficiency as revealed by chlorosis and decreased biomass, was correlated with lower FC-R activity and lower organic acid level in leaf cells, which could cause a decreased Fe mobility and trigger other Fe-stress responses in this organ to enhance acidification and Fe uptake inside cells; and (3) the chlorosis paradox phenomenon in citrus likely occurs as a combination of a marked FC-R activity impairment in the leaf and the strong growth inhibition in this organ.

Allelic Variation of NtNramp5 Associated with Cultivar Variation in Cadmium Accumulation in Tobacco

Tobacco (Nicotiana tabacum) is a cadmium (Cd) accumulator, and smoking is a major source of Cd exposure. In the present study, we identified two tobacco cultivars with contrasting phenotypes of Cd and manganese (Mn) accumulation in both hydroponic and soil pot experiments. Physiological experiments showed that the two cultivars differed in Cd uptake, but not in Cd translocation from roots to shoots. A homolog of OsNramp5 (natural resistance-associated macrophage protein 5), NtNramp5, was isolated from both cultivars. There was no significant difference in the expression level of NtNramp5 in the roots between the two cultivars. Sequence analysis revealed that the low Cd/Mn-accumulating cultivar possesses an NtNramp5 allele with a predicted mutation for early translation termination, resulting in a truncated protein missing 104 amino acids in the C-terminus of the full-length NtNramp5 found in the high Cd/Mn-accumulating cultivar. Both proteins were found to be localized to the plasma membrane. Heterologous expression of the two alleles of NtNramp5 in yeast showed that the full-length protein had transport activities for both Mn and Cd, whereas the truncated protein had no transport activity for Mn and a weak transport activity for Cd. These results suggest that NtNramp5 is a transporter for Mn and Cd, and the allelic variation in the coding region of NtNramp5 probaby explains the cultivar difference in Cd and Mn accumulation.

Finger on the Pulse: Pumping Iron into Chickpea

Iron deficiency is a major problem in both developing and developed countries, and much of this can be attributed to insufficient dietary intake. Over the past decades several measures, such as supplementation and food fortification, have helped to alleviate this problem. However, their associated costs limit their accessibility and effectiveness, particularly amongst the financially constrained. A more affordable and sustainable option that can be implemented alongside existing measures is biofortification. To date, much work has been invested into staples like cereals and root crops-this has culminated in the successful generation of high iron-accumulating lines in rice and pearl millet. More recently, pulses have gained attention as targets for biofortification. Being secondary staples rich in protein, they are a nutritional complement to the traditional starchy staples. Despite the relative youth of this interest, considerable advances have already been made concerning the biofortification of pulses. Several studies have been conducted in bean, chickpea, lentil, and pea to assess existing germplasm for high iron-accumulating traits. However, little is known about the molecular workings behind these traits, particularly in a leguminous context, and biofortification via genetic modification (GM) remains to be attempted. This review examines the current state of the iron biofortification in pulses, particularly chickpea. The challenges concerning biofortification in pulses are also discussed. Specifically, the potential application of transgenic technology is explored, with focus on the genes that have been successfully used in biofortification efforts in rice.

Genome Wide Identification of Orthologous ZIP Genes Associated with Zinc and Iron Translocation in Setaria italica

Genes in the ZIP family encode transcripts to store and transport bivalent metal micronutrient, particularly iron (Fe) and or zinc (Zn). These transcripts are important for a variety of functions involved in the developmental and physiological processes in many plant species, including most, if not all, Poaceae plant species and the model species Arabidopsis. Here, we present the report of a genome wide investigation of orthologous ZIP genes in Setaria italica and the identification of 7 single copy genes. RT-PCR shows 4 of them could be used to increase the bio-availability of zinc and iron content in grains. Of 36 ZIP members, 25 genes have traces of signal peptide based sub-cellular localization, as compared to those of plant species studied previously, yet translocation of ions remains unclear. In silico analysis of gene structure and protein nature suggests that these two were preeminent in shaping the functional diversity of the ZIP gene family in S. italica. NAC, bZIP and bHLH are the predominant Fe and Zn responsive transcription factors present in SiZIP genes. Together, our results provide new insights into the signal peptide based/independent iron and zinc translocation in the plant system and allowed identification of ZIP genes that may be involved in the zinc and iron absorption from the soil, and thus transporting it to the cereal grain underlying high micronutrient accumulation.

Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks

BACKGROUND

FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is the central regulator of iron uptake in Arabidopsis thaliana roots. We performed transcriptome analyses of six day-old seedlings and roots of six week-old plants using wild type, a fit knock-out mutant and a FIT over-expression line grown under iron-sufficient or iron-deficient conditions. We compared genes regulated in a FIT-dependent manner depending on the developmental stage of the plants. We assembled a high likelihood dataset which we used to perform co-expression and functional analysis of the most stably iron deficiency-induced genes.

RESULTS

448 genes were found FIT-regulated. Out of these, 34 genes were robustly FIT-regulated in root and seedling samples and included 13 novel FIT-dependent genes. Three hundred thirty-one genes showed differential regulation in response to the presence and absence of FIT only in the root samples, while this was the case for 83 genes in the seedling samples. We assembled a virtual dataset of iron-regulated genes based on a total of 14 transcriptomic analyses of iron-deficient and iron-sufficient wild-type plants to pinpoint the best marker genes for iron deficiency and analyzed this dataset in depth. Co-expression analysis of this dataset revealed 13 distinct regulons part of which predominantly contained functionally related genes.

CONCLUSIONS

We could enlarge the list of FIT-dependent genes and discriminate between genes that are robustly FIT-regulated in roots and seedlings or only in one of those. FIT-regulated genes were mostly induced, few of them were repressed by FIT. With the analysis of a virtual dataset we could filter out and pinpoint new candidates among the most reliable marker genes for iron deficiency. Moreover, co-expression and functional analysis of this virtual dataset revealed iron deficiency-induced and functionally distinct regulons.

Understanding the regulation of iron nutrition: can it contribute to improving iron toxicity tolerance in rice?

Iron nutrition in plants is highly regulated in order to supply amounts sufficient for optimal growth while preventing deleterious effects. In response to iron deficiency, plants induce either reduction-based or chelation-based mechanisms to enhance iron uptake from the soil. Major physiological traits and genes involved in these mechanisms have been fairly well described in model plants like Arabidopsis thaliana (L. Heynh.) and rice (Oryza sativa L.). However, for rice, iron toxicity presents a major challenge worldwide and causes yield reductions because rice is widely cultivated in flooded soils. Nonetheless, rice employs different mechanisms of adaptation to iron-toxicity, which range from avoidance to tissue tolerance. The physiological and molecular bases of such mechanisms have not been fully investigated and their use in breeding for iron-toxicity tolerance remains limited. Efforts to precisely characterise iron-toxicity control mechanisms may help speed-up the development of tolerant rice varieties. Considering how far the understanding of iron dynamics in the soil and plants has progressed, we consider it valuable to exploit such knowledge to improve rice tolerance to iron toxicity. Here we present the mechanisms that regulate iron uptake from the rhizosphere to the plant tissues together with the possible regulators involved. In addition, a genetic model for iron-toxicity tolerance in rice, which hypothesises possible modulation of key genes involved in iron nutrition and regulation is presented. The possibility of incorporating such relevant regulators in breeding is also discussed.

Vacuolar compartmentalization as indispensable component of heavy metal detoxification in plants

Plant cells orchestrate an array of molecular mechanisms for maintaining plasmatic concentrations of essential heavy metal (HM) ions, for example, iron, zinc and copper, within the optimal functional range. In parallel, concentrations of non-essential HMs and metalloids, for example, cadmium, mercury and arsenic, should be kept below their toxicity threshold levels. Vacuolar compartmentalization is central to HM homeostasis. It depends on two vacuolar pumps (V-ATPase and V-PPase) and a set of tonoplast transporters, which are directly driven by proton motive force, and primary ATP-dependent pumps. While HM non-hyperaccumulator plants largely sequester toxic HMs in root vacuoles, HM hyperaccumulators usually sequester them in leaf cell vacuoles following efficient long-distance translocation. The distinct strategies evolved as a consequence of organ-specific differences particularly in vacuolar transporters and in addition to distinct features in long-distance transport. Recent molecular and functional characterization of tonoplast HM transporters has advanced our understanding of their contribution to HM homeostasis, tolerance and hyperaccumulation. Another important part of the dynamic vacuolar sequestration syndrome involves enhanced vacuolation. It involves vesicular trafficking in HM detoxification. The present review provides an updated account of molecular aspects that contribute to the vacuolar compartmentalization of HMs.

In silico analysis of Mn transporters (NRAMP1) in various plant species

Manganese (Mn) is an essential micronutrient in plant life cycle. It may be involved in photosynthesis, carbohydrate and lipid biosynthesis, and oxidative stress protection. Mn deficiency inhibits the plant growth and development, and causes the various plant symptoms such as interveinal chlorosis and tissue necrosis. Despite its importance in plant life cycle, we still have limited knowledge about Mn transporters in many plant species. Therefore, this study aimed to identify and characterize high affinity Arabidopsis Mn root transporter NRAMP1 orthologs in 17 different plant species. Various in silico methods and digital gene expression data were used in identification and characterization of NRAMP1 homologs; physico-chemical properties of sequences were calculated, putative transmembrane domains (TMDs) and conserved motif signatures were determined, phylogenetic tree was constructed, 3D models and interactome map were generated, and gene expression data was analyzed. 49 NRAMP1 homologs were identified from proteome datasets of 17 plant species using AtNRAMP1 as query. Identified sequences were characterized with a NRAMP domain structure, 10-12 putative TMDs with cytosolic N- and C-terminuses, and 10-14 exons encoding a protein of 500-588 amino acids and 53.8-64.3 kDa molecular weight with basic characteristics. Consensus transport residues, GQSSTITGTYAGQY(/F)V(/I)MQGFLD(/E/N) between TMD-8 and 9 were identified in all sequences but putative N-linked glycosylation sites were not highly conserved. In phylogeny, NRAMP1 sequences demonstrated divergence in lower and higher plants as well as in monocots and dicots. Despite divergence of lower plant Physcomitrella patens in phylogeny, it showed similarity in superposed 3D models. Phylogenetic distribution of AtNRAMP1 and 6 homologs inferred a functional relationship to NRAMP6 sequences in Mn transport, while distribution of OsNRAMP1 and 5 homologs implicated an involvement of NRAMP1 sequences in Mn transport or a cross-talk between in Fe-Mn homeostasis. Interactome analysis further confirmed this cross-talk between Mn and Fe pathways. Gene expression profile of AtNRAMP1 under Fe-, K-, P- and S-deficiencies, and cold, drought, heat and salt stresses revealed various proteins involving in transcription regulation, cofactor biosynthesis, diverse developmental roles, carbohydrate metabolism, oxidation-reduction reactions, cellular signaling and protein degradation pathways. Mn deficiency or toxicity could cause serious adverse effects in plants as well as in humans. To reduce these adversities mainly rely on understanding the molecular mechanisms underlying Mn uptake from the soil. However, we still have limited knowledge regarding the structural and functional roles of Mn transporters in many plant species. Therefore, identification and characterization of Mn root uptake transporter, NRAMP1 orthologs in various plant species will provide valuable theoretical knowledge to better understand Mn transporters as well as it may become an insight for future studies aiming to develop genetically engineered and biofortified plants.