A FIT-binding protein is involved in modulating iron and zinc homeostasis in Arabidopsis

The transcription factor bZIP44 cooperates with MYB10 and MYB72 to regulate the response of Arabidopsis thaliana to iron deficiency stress

Nicotianamine (NA) plays a crucial role in transporting metal ions, including iron (Fe), in plants; therefore, NICOTIANAMINE SYNTHASE (NAS) genes, which control NA synthesis, are tightly regulated at the transcriptional level. However, the transcriptional regulatory mechanisms of NAS genes require further investigations. In this study, we determined the role of bZIP44 in mediating plant response to Fe deficiency stress by conducting transformation experiments and assays. bZIP44 positively regulated the response of Arabidopsis to Fe deficiency stress by interacting with MYB10 and MYB72 to enhance their abilities to bind at NAS2 and NAS4 promoters, thereby increasing NAS2 and NAS4 transcriptional levels and promote NA synthesis. In summary, the transcription activities of bZIP44, MYB10, and MYB72 were induced in response to Fe deficiency stress, which enhanced the interaction between bZIP44 and MYB10 or MYB72 proteins, synergistically activated the transcriptional activity of NAS2 and NAS4, promoted NA synthesis, and improved Fe transport, thereby enhancing plant tolerance to Fe deficiency stress.

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.

Functions of Basic Helix-Loop-Helix (bHLH) Proteins in the Regulation of Plant Responses to Cold, Drought, Salt, and Iron Deficiency: A Comprehensive Review

Abiotic stresses including cold, drought, salt, and iron deficiency severely impair plant development, crop productivity, and geographic distribution. Several bodies of research have shed light on the pleiotropic functions of BASIC HELIX-LOOP-HELIX (bHLH) proteins in plant responses to these abiotic stresses. In this review, we mention the regulatory roles of bHLH TFs in response to stresses such as cold, drought, salt resistance, and iron deficiency, as well as in enhancing grain yield in plants, especially crops. The bHLH proteins bind to E/G-box motifs in the target promoter and interact with various other factors to form a complex regulatory network. Through this network, they cooperatively activate or repress the transcription of downstream genes, thereby regulating various stress responses. Finally, we present some perspectives for future research focusing on the molecular mechanisms that integrate and coordinate these abiotic stresses. Understanding these molecular mechanisms is crucial for the development of stress-tolerant crops.

Integrated BSA-seq and RNA-seq analysis to identify candidate genes associated with nitrogen utilization efficiency (NUtE) in rapeseed (Brassica napus L.)

Rapeseed (Brassica napus L.) is one of the important oil crops, with a high demand for nitrogen (N). It is essential to explore the potential of rapeseed to improve nitrogen utilization efficiency (NUtE). Rapeseed is an allotetraploid crop with a relatively large and complex genome, and there are few studies on the mapping of genes related to NUtE regulation. In this study, we used the combination of bulk segregant analysis sequencing (BSA-Seq) and RNA sequencing (RNA-Seq) to analyze the N-efficient genotype 'Zheyou 18' and N-inefficient genotype 'Sollux', to identify the genetic regulatory mechanisms. Several candidate genes were screened, such as the high-affinity nitrate transporter gene NRT2.1 (BnaC08g43370D) and the abscisic acid (ABA) signal transduction-related genes (BnaC02g14540D, BnaA03g20760D, and BnaA05g01330D). BnaA05g01330D was annotated as ABA-INDUCIBLE bHLH-TYPE TRANSCRIPTION FACTOR (AIB/bHLH17), which was highly expressed in the root. The results showed that the primary root length of the ataib mutant was significantly longer than that of the wild type under low N conditions. Overexpression of BnaA5.AIB could reduce the NUtE under low N levels in Arabidopsis (Arabidopsis thaliana). Candidate genes identified in this study may be involved in the regulation of NUtE in rapeseed, and new functions of AIB in orchestrating N uptake and utilization have been revealed. It is indicated that BnaA5.AIB may be the key factor that links ABA to N signaling and a negative regulator of NUtE. It will provide a theoretical basis and application prospect for resource conservation, environmental protection, and sustainable agricultural development.

BRUTUS-LIKE (BTSL) E3 ligase-mediated fine-tuning of Fe regulation negatively affects Zn tolerance of Arabidopsis

The mineral micronutrients zinc (Zn) and iron (Fe) are essential for plant growth and human nutrition, but interactions between the homeostatic networks of these two elements are not fully understood. Here we show that loss of function of BTSL1 and BTSL2, which encode partially redundant E3 ubiquitin ligases that negatively regulate Fe uptake, confers tolerance to Zn excess in Arabidopsis thaliana. Double btsl1 btsl2 mutant seedlings grown on high Zn medium accumulated similar amounts of Zn in roots and shoots to the wild type, but suppressed the accumulation of excess Fe in roots. RNA-sequencing analysis showed that roots of mutant seedlings had relatively higher expression of genes involved in Fe uptake (IRT1, FRO2, and NAS) and in Zn storage (MTP3 and ZIF1). Surprisingly, mutant shoots did not show the transcriptional Fe deficiency response which is normally induced by Zn excess. Split-root experiments suggested that within roots the BTSL proteins act locally and downstream of systemic Fe deficiency signals. Together, our data show that constitutive low-level induction of the Fe deficiency response protects btsl1 btsl2 mutants from Zn toxicity. We propose that BTSL protein function is disadvantageous in situations of external Zn and Fe imbalances, and formulate a general model for Zn-Fe interactions in plants.

Iron and zinc homeostasis in plants: a matter of trade-offs

This article comments on:

Stanton C, Rodríguez-Celma J, Krämer U, Sanders D, Balk J. 2023. BRUTUS-LIKE (BTSL) E3 ligase-mediated fine-tuning of Fe regulation negatively affects Zn tolerance of Arabidopsis. Journal of Experimental Botany 74, 5767–5782.

The transcription factor MYC1 interacts with FIT to negatively regulate iron homeostasis in Arabidopsis thaliana

Iron (Fe) is an indispensable trace mineral element for the normal growth of plants, and it is involved in different biological processes; Fe shortage in plants can induce chlorosis and yield loss. The objective of this research is to identify novel genes that participated in the regulation of Fe-deficiency stress in Arabidopsis thaliana. A basic helix-loop-helix (bHLH) transcription factor (MYC1) was identified to be interacting with the FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) using a yeast-two-hybrid assay. Transcript-level analysis showed that there was a decrease in MYC1 expression in Arabidopsis to cope with Fe-deficiency stress. Functional deficiency of MYC1 in Arabidopsis leads to an increase in Fe-deficiency tolerance and Fe-accumulation, whereas MYC1-overexpressing plants have an enhanced sensitivity to Fe-deficiency stress. Additionally, MYC1 inhibited the formation of FIT and bHLH38/39 heterodimers, which suppressed the expressed level for Fe acquisition genes FRO2 and IRT1 during Fe-deficiency stress. These results showed that MYC1 functions as a negative modulator of the Fe-deficiency stress response by inhibiting the formation of FIT and bHLH38/39 heterodimers, thereby suppressing the binding of FIT and bHLH38/39 heterodimers to the promoters of FRO2 and IRT1 to modulate Fe intake during Fe-deficiency stress. Overall, the findings of this study elucidated the role of MYC1 in coping with Fe-deficiency stress, and provided potential targets for the developing of crop varieties resistant to Fe-deficiency stress.

Biofortification to avoid malnutrition in humans in a changing climate: Enhancing micronutrient bioavailability in seed, tuber, and storage roots

Malnutrition results in enormous socio-economic costs to the individual, their community, and the nation's economy. The evidence suggests an overall negative impact of climate change on the agricultural productivity and nutritional quality of food crops. Producing more food with better nutritional quality, which is feasible, should be prioritized in crop improvement programs. Biofortification refers to developing micronutrient -dense cultivars through crossbreeding or genetic engineering. This review provides updates on nutrient acquisition, transport, and storage in plant organs; the cross-talk between macro- and micronutrients transport and signaling; nutrient profiling and spatial and temporal distribution; the putative and functionally characterized genes/single-nucleotide polymorphisms associated with Fe, Zn, and β-carotene; and global efforts to breed nutrient-dense crops and map adoption of such crops globally. This article also includes an overview on the bioavailability, bioaccessibility, and bioactivity of nutrients as well as the molecular basis of nutrient transport and absorption in human. Over 400 minerals (Fe, Zn) and provitamin A-rich cultivars have been released in the Global South. Approximately 4.6 million households currently cultivate Zn-rich rice and wheat, while ~3 million households in sub-Saharan Africa and Latin America benefit from Fe-rich beans, and 2.6 million people in sub-Saharan Africa and Brazil eat provitamin A-rich cassava. Furthermore, nutrient profiles can be improved through genetic engineering in an agronomically acceptable genetic background. The development of "Golden Rice" and provitamin A-rich dessert bananas and subsequent transfer of this trait into locally adapted cultivars are evident, with no significant change in nutritional profile, except for the trait incorporated. A greater understanding of nutrient transport and absorption may lead to the development of diet therapy for the betterment of human health.

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.

Requirement and functional redundancy of two large ribonucleotide reductase subunit genes for cell cycle, chloroplast biogenesis and photosynthesis in tomato

BACKGROUND AND AIMS

Ribonucleotide reductase (RNR), functioning in the de novo synthesis of deoxyribonucleoside triphosphates (dNTPs), is crucial for DNA replication and cell cycle progression. In most plants, the large subunits of RNR have more than one homologous gene. However, the different functions of these homologous genes in plant development remain unknown. In this study, we obtained the mutants of two large subunits of RNR in tomato and studied their functions.

METHODS

The mutant ylc1 was obtained by ethyl methyl sulfonate (EMS) treatment. Through map-based cloning, complementation and knock-out experiments, it was confirmed that YLC1 encodes a large subunit of RNR (SlRNRL1). The expression level of the genes related to cell cycle progression, chloroplast biogenesis and photosynthesis was assessed by RNA-sequencing. In addition, we knocked out SlRNRL2 (a SlRNRL1 homologue) using CRISPR-Cas9 technology in the tomato genome, and we down-regulated SlRNRL2 expression in the genetic background of slrnrl1-1 using a tobacco rattle virus-induced gene silencing (VIGS) system.

KEY RESULTS

The mutant slrnrl1 exhibited dwarf stature, chlorotic young leaves and smaller fruits. Physiological and transcriptomic analyses indicated that SlRNRL1 plays a crucial role in the regulation of cell cycle progression, chloroplast biogenesis and photosynthesis in tomato. The slrnrl2 mutant did not exhibit any visible phenotype. SlRNRL2 has a redundant function with SlRNRL1, and the double mutant slrnrl1slrnrl2 is lethal.

CONCLUSIONS

SlRNRL1 is essential for cell cycle progression, chloroplast biogenesis and photosynthesis. In addition, SlRNRL1 and SlRNRL2 possess redundant functions and at least one of these RNRLs is required for tomato survival, growth and development.

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.

Long-distance mobile mRNA CAX3 modulates iron uptake and zinc compartmentalization

Iron deficiency in plants can lead to excessive absorption of zinc; however, important details of this mechanism have yet to be elucidated. Here, we report that MdCAX3 mRNA is transported from the leaf to the root, and that MdCAX3 is then activated by MdCXIP1. Suppression of MdCAX3 expression leads to an increase in the root apoplastic pH, which is associated with the iron deficiency response. Notably, overexpression of MdCAX3 does not affect the apoplastic pH in a MdCXIP1 loss-of-function Malus baccata (Mb) mutant that has a deletion in the MdCXIP1 promoter. This deletion in Mb weakens MdCXIP1 expression. Co-expression of MdCAX3 and MdCXIP1 in Mb causes a decrease in the root apoplastic pH. Furthermore, suppressing MdCAX3 in Malus significantly reduces zinc vacuole compartmentalization. We also show that MdCAX3 activated by MdCXIP1 is not only involved in iron uptake, but also in regulating zinc detoxification by compartmentalizing zinc in vacuoles to avoid iron starvation-induced zinc toxicity. Thus, mobile MdCAX3 mRNA is involved in the regulation of iron and zinc homeostasis in response to iron starvation.

Cross-Talks Between Macro- and Micronutrient Uptake and Signaling in Plants

In nature, land plants as sessile organisms are faced with multiple nutrient stresses that often occur simultaneously in soil. Nitrogen (N), phosphorus (P), sulfur (S), zinc (Zn), and iron (Fe) are five of the essential nutrients that affect plant growth and health. Although these minerals are relatively inaccessible to plants due to their low solubility and relative immobilization, plants have adopted coping mechanisms for survival under multiple nutrient stress conditions. The double interactions between N, Pi, S, Zn, and Fe have long been recognized in plants at the physiological level. However, the molecular mechanisms and signaling pathways underlying these cross-talks in plants remain poorly understood. This review preliminarily examined recent progress and current knowledge of the biochemical and physiological interactions between macro- and micro-mineral nutrients in plants and aimed to focus on the cross-talks between N, Pi, S, Zn, and Fe uptake and homeostasis in plants. More importantly, we further reviewed current studies on the molecular mechanisms underlying the cross-talks between N, Pi, S, Zn, and Fe homeostasis to better understand how these nutrient interactions affect the mineral uptake and signaling in plants. This review serves as a basis for further studies on multiple nutrient stress signaling in plants. Overall, the development of an integrative study of multiple nutrient signaling cross-talks in plants will be of important biological significance and crucial to sustainable agriculture.

Fe acquisition at the crossroad of calcium and reactive oxygen species signaling

Due to its redox properties, iron is both essential and toxic. Therefore, soil iron availability variations pose a significant problem for plants. Recent evidence suggests that calcium and reactive oxygen species coordinate signaling events related to soil iron acquisition. Calcium was found to affect directly IRT1-mediated iron import through the lipid-binding protein EHB1 and to trigger a CBL-CIPK-mediated signaling influencing the activity of the key iron-acquisition transcription factor FIT. In parallel, under prolonged iron deficiency, reactive oxygen species both inhibit FIT function and depend on FIT through the function of the catalase CAT2. We discuss the role of calcium and reactive oxygen species signaling in iron acquisition, with post-translational mechanisms influencing the localization and activity of iron-acquisition regulators and effectors.

FIT and bHLH Ib transcription factors modulate iron and copper crosstalk in Arabidopsis

Although the crosstalk between iron (Fe) and copper (Cu) homeostasis signalling networks exists in plants, the underlined molecular mechanism remains unclear. FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) and four bHLH Ib members (bHLH38, bHLH39, bHLH100 and bHLH101) are the key regulators of Fe homeostasis. Here, we reveal that FIT and bHLH Ib control the up-regulation of Cu-uptake genes (COPT2, FRO4 and FRO5) by Fe deficiency, and Cu is required for improving plant growth under Fe-deficiency conditions. The induction of Cu-uptake gene expression and the elevation of Cu concentration are inhibited in the fit-2 or bhlh4x (the quadruple mutant of four bHLH Ib genes) under Fe-deficiency conditions. The dual overexpression of both bHLH38 (or bHLH39) and FIT activates the expression of COPT2, FRO4 and FRO5 and increases Cu accumulation. Furthermore, bHLH Ib proteins directly bind to the promoters of COPT2, FRO4 and FRO5. Either Cu supplement or overexpression of COPT2 or FRO4 improves the growth of fit-2 under Fe-deficiency conditions. Moreover, the induction of COPT2, FRO4 and FRO5 by Fe deficiency is independent of SPL7, a central regulator of Cu-deficiency responses. This work through the link between bHLH Ib/FIT and COPT2/FRO4/FRO5 under Fe-deficiency conditions establishes a new relationship between Cu and Fe homeostasis.

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.

A novel zinc transporter essential for Arabidopsis zinc and iron-dependent growth

Zinc (Zn), an essential micronutrient, is absorbed by plant roots and redistributed to leaves. This process must be finely regulated in order to avoid toxic Zn²⁺ overaccumulation, which can arise due to Zn²⁺ oversupply or Zn²⁺ hyperaccumulation induced by Fe²⁺ deficiency. Although several proteins in Arabidopsis thaliana are essential for retaining Zn in the root and partitioning it from roots to leaves, how Zn²⁺ homeostasis in leaves is maintained is largely unknown. In this study, we identified a novel Golgi-localized protein named ZINC NUTRIENT ESSENTIAL1 (AtZNE1,At3g08650) in Arabidopsis. AtZNE1 contains 14 putative transmembrane domains. AtZNE1 promoter has strong activity in the root and leaf. Its expression complemented the increased sensitivity of a yeast mutant to excess Zn²⁺. The disruption of AtZNE1 in the T-DNA insertion mutant atzne1 caused growth defect under excess-Zn or Fe deficit conditions, but had no effects on the total Zn and Fe contents. We propose that AtZNE1 plays a vital role in plant adaptation to excess Zn or Fe deficiency.

Dissection of Molecular Processes and Genetic Architecture Underlying Iron and Zinc Homeostasis for Biofortification: From Model Plants to Common Wheat

The micronutrients iron (Fe) and zinc (Zn) are not only essential for plant survival and proliferation but are crucial for human health. Increasing Fe and Zn levels in edible parts of plants, known as biofortification, is seen a sustainable approach to alleviate micronutrient deficiency in humans. Wheat, as one of the leading staple foods worldwide, is recognized as a prioritized choice for Fe and Zn biofortification. However, to date, limited molecular and physiological mechanisms have been elucidated for Fe and Zn homeostasis in wheat. The expanding molecular understanding of Fe and Zn homeostasis in model plants is providing invaluable resources to biofortify wheat. Recent advancements in NGS (next generation sequencing) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms have initiated a revolution in resources and approaches for wheat genetic investigations and breeding. Here, we summarize molecular processes and genes involved in Fe and Zn homeostasis in the model plants Arabidopsis and rice, identify their orthologs in the wheat genome, and relate them to known wheat Fe/Zn QTL (quantitative trait locus/loci) based on physical positions. The current study provides the first inventory of the genes regulating grain Fe and Zn homeostasis in wheat, which will benefit gene discovery and breeding, and thereby accelerate the release of Fe- and Zn-enriched wheats.

bHLH121 Functions as a Direct Link that Facilitates the Activation of FIT by bHLH IVc Transcription Factors for Maintaining Fe Homeostasis in Arabidopsis

Iron (Fe) deficiency is prevalent in plants grown in neutral or alkaline soil. Plants have evolved sophisticated mechanisms that regulate Fe homeostasis, ensuring survival. In Arabidopsis, FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) is a crucial regulator of Fe-deficiency response. FIT is activated indirectly by basic helix-loop-helix (bHLH) IVc transcription factors (TFs) under Fe deficiency; however, it remains unclear which protein(s) act as the linker to mediate the activation of FIT by bHLH IVc TFs. In this study, we characterize the functions of bHLH121 and demonstrate that it directly associates with the FIT promoter. We found that loss-of-function mutations of bHLH121 cause severe Fe-deficiency symptoms, reduced Fe accumulation, and disrupted expression of genes associated with Fe homeostasis. Genetic analysis showed that FIT is epistatic to bHLH121 and FIT overexpression partially rescues the bhlh121 mutant. Further investigations revealed that bHLH IVc TFs interact with and promote nuclear accumulation of bHLH121. We demonstrated that bHLH121 has DNA-binding activity and can bind the promoters of the FIT and bHLH Ib genes, but we did not find that it has either direct transcriptional activation or repression activity toward these genes. Meanwhile, we found that bHLH121 functions downstream of and is a direct target of bHLH IVc TFs, and its expression is induced by Fe deficiency in a bHLH IVc-dependent manner. Taken together, these results establish that bHLH121 functions together with bHLH IVc TFs to positively regulate the expression of FIT and thus plays a pivotal role in maintaining Fe homeostasis in Arabidopsis.

Identification of Novel Genomic Regions and Superior Alleles Associated with Zn Accumulation in Wheat Using a Genome-Wide Association Analysis Method

Micronutrient deficiencies, and especially zinc (Zn) deficiency, pose serious health problems to people who mainly depend on cereal-based diets. Here, we performed a genome-wide association study (GWAS) to detect the genetic basis of the Zn accumulation in wheat (Triticum aestivum L.) grains with a diversity panel of 207 bread wheat varieties. To uncover authentic quantitative trait loci (QTL) controlling Zn accumulation, the varieties were planted in three locations. In total, 29 unique loci associated with Zn grain accumulation were identified. Notably, seven non-redundant loci located on chromosomes 1B, 3B, 3D, 4A, 5A, 5B, and 7A, were detected at least in two environments. Of these quantitative trait loci (QTL), six coincided with known QTL or genes, whereas the highest effect QTL on chromosome 3D identified in this study was not reported previously. Searches of public databases revealed that the seven identified QTL coincided with seven putative candidate genes linked to Zn accumulation. Among these seven genes, NAC domain-containing protein gene (TraesCS3D02G078500) linked with the most significant single nucleotide polymorphism (SNP) AX-94729264 on chromosome 3D was relevant to metal accumulation in wheat grains. Results of this study provide new insights into the genetic architecture of Zn accumulation in wheat grains.

Maize NAC-domain retained splice variants act as dominant negatives to interfere with the full-length NAC counterparts

The plant-specific NAC transcription factors play diverse roles in various stress signaling. Alternative splicing is particularly prevalent in plants under stress. However, the investigation of cadmium (Cd) on the differential expression of the splice variants of NACs is in its infancy. Here, we identified three Cd-induced intron retention splice NAC variants which only contained the canonical NAC domain, designated as nacDomains, derived from three Cd-upregulated maize NACs. Subcellular localization analysis indicated that both nacDomain and its full-length NAC counterpart co-localized in the nucleus as manifested in the BiFC assay, thus implied that nacDomains and their corresponding NACs form heterodimers through the identical NAC domain. Further chimeric reporter/effector transient expression assay and Cd-tolerance assay in tobacco leaves collectively indicated that nacDomain-NAC heterodimers were involved in the regulation of NAC function. The results obtained here were in accordance with the model of dominant negative, which suggested that nacDomain act as the dominant negative to antagonize the regulation of NAC on its target gene expression and the Cd-tolerance function performance of NAC transcription factor. These findings proposed a novel insight into understanding the molecular mechanisms of Cd response in plants.

Understanding the Complexity of Iron Sensing and Signaling Cascades in Plants

Under iron-deficient conditions, plants induce the expression of a set of genes involved in iron uptake and translocation. This response to iron deficiency is regulated by transcriptional networks mediated by transcription factors (TFs) and protein-level modification of key factors by ubiquitin ligases. Several of the basic helix-loop-helix TFs and the HRZ/BTS ubiquitin ligases are conserved across graminaceous and non-graminaceous plants. Other regulators are specific, such as IDEF1 and IDEF2 in graminaceous plants and FIT/FER and MYB10/72 in non-graminaceous plants. IMA/FEP peptides positively regulate the iron-deficiency responses in a wide range of plants by unknown mechanisms. Direct binding of iron or other metals to some key regulators, including HRZ/BTS and IDEF1, may be responsible for intracellular iron-sensing and -signaling events. In addition, key TFs such as FIT and IDEF1 interact with various proteins involved in signaling pathways of plant hormones, oxidative stress and metal abundance. Thus, FIT and IDEF1 might function as hubs for the integration of environmental signals to modulate the responses to iron deficiency. In addition to local iron signaling, root iron responses are modulated by shoot-derived long-distance signaling potentially mediated by phloem-mobile substances such as iron, iron chelates and IMA/FEP peptides.

Spatiotemporal heterogeneity of photosystem II function during acclimation to zinc exposure and mineral nutrition changes in the hyperaccumulator Noccaea caerulescens

We investigated changes in mineral nutrient uptake and translocation and photosystem II (PSII) functionality, in the hyperaccumulator Noccaea caerulescens after exposure to 800 μM Zn in hydroponic culture. Exposure to Zn inhibited the uptake of K, Mn, Cu, Ca, and Mg, while the uptake of Fe and Zn enhanced. Yet, Ca and Mg aboveground tissue concentrations remain unchanged while Cu increased significantly. In the present study, we provide new data on the mechanism of N. caerulescens acclimation to Zn exposure by elucidating the process of photosynthetic acclimation. A spatial heterogeneity in PSII functionality in N. caerulescens leaves exposed to Zn for 3 days was detected, while a threshold time of 4 days was needed for the activation of Zn detoxification mechanism(s) to decrease Zn toxicity and for the stomatal closure to decrease Zn supply at the severely affected leaf area. After 10-day exposure to Zn, the allocation of absorbed light energy in PSII under low light did not differ compared to control ones, while under high light, the quantum yield of non-regulated energy loss in PSII (Φ_NO) was lower than the control, due to an efficient photoprotective mechanism. The chlorophyll fluorescence images of non-photochemical quenching (NPQ) and photochemical quenching (q_p) clearly showed spatial and temporal heterogeneity in N. caerulescens exposure to Zn and provided further information on the particular leaf area that was most sensitive to heavy metal stress. We propose the use of chlorophyll fluorescence imaging, and in particular the redox state of the plastoquinone (PQ) pool that was found to display the highest spatiotemporal heterogeneity, as a sensitive bio-indicator to measure the environmental pressure by heavy metals on plants.

FIT-Binding Proteins and Their Functions in the Regulation of Fe Homeostasis

Iron, as an essential micronutrient, is required by all living organisms. In plants, the deficiency and excess of iron will impair their growth and development. For maintaining a proper intracellular iron concentration, plants evolved different regulation mechanisms to tightly control iron uptake, translocation and storage. FIT, a bHLH transcription factor, is the master regulator of the iron deficiency responses and homeostasis in Arabidopsis. It interacts with different proteins, functioning in controlling the expression of various genes involved in iron uptake and homeostasis. In this review, we summarize the recent progress in the studies of FIT and FIT-binding proteins, and give an overview of FIT-regulated network in iron deficiency response and homeostasis.

Four IVa bHLH Transcription Factors Are Novel Interactors of FIT and Mediate JA Inhibition of Iron Uptake in Arabidopsis

Plants have evolved sophisticated genetic networks to regulate iron (Fe) homeostasis for their survival. Several classes of plant hormones including jasmonic acid (JA) have been shown to be involved in regulating the expression of iron uptake and/or deficiency-responsive genes in plants. However, the molecular mechanisms by which JA regulates iron uptake remain unclear. In this study, we found that JA negatively modulates iron uptake by downregulating the expression of FIT (bHLH29), bHLH38, bHLH39, bHLH100, and bHLH101 and promoting the degradation of FIT protein, a key regulator of iron uptake in Arabidopsis. We further demonstrated that the subgroup IVa bHLH proteins, bHLH18, bHLH19, bHLH20, and bHLH25, are novel interactors of FIT, which promote JA-induced FIT protein degradation. These four IVa bHLHs function redundantly to antagonize the activity of the Ib bHLHs (such as bHLH38) in regulating FIT protein stability under iron deficiency. The four IVa bHLH genes are primarily expressed in roots, and are inducible by JA treatment. Moreover, we found that MYC2 and JAR1, two critical components of the JA signaling pathway, play critical roles in mediating JA suppression of the expression of FIT and Ib bHLH genes, whereas they differentially modulate the expression of bHLH18, bHLH19, bHLH20, and bHLH25 to regulate FIT accumulation under iron deficiency. Taken together, these results indicate that by transcriptionally regulating the expression of different sets of bHLH genes JA signaling promotes FIT degradation, resulting in reduced expression of iron-uptake genes, IRT1 and FRO2, and increased sensitivity to iron deficiency. Our data suggest that there is a multilayered inhibition of iron-deficiency response in the presence JA in Arabidopsis.

The Arabidopsis bZIP19 and bZIP23 Activity Requires Zinc Deficiency - Insight on Regulation From Complementation Lines

All living organisms require zinc as an essential micronutrient. Maintaining appropriate intracellular zinc supply, and avoiding deficiency or toxic excess, requires a tight regulation of zinc homeostasis. In Arabidopsis, bZIP19 and bZIP23 (basic-leucine zipper) transcription factors are the central regulators of the zinc deficiency response. Their targets include members of the ZIP (Zrt/Irt-like Protein) transporter family, involved in cellular zinc uptake, which are up-regulated at zinc deficiency. However, the mechanisms by which these transcription factors are regulated by cellular zinc status are not yet known. Here, to further our insight, we took advantage of the zinc deficiency hypersensitive phenotype of the bzip19 bzip23 double mutant, and used it as background to produce complementation lines of each Arabidopsis F-bZIP transcription factor, including bZIP24. On these lines, we performed complementation and localization studies, analyzed the transcript level of a subset of putative target genes, and performed elemental tissue profiling. We find evidence supporting that the zinc-dependent activity of bZIP19 and bZIP23 is modulated by zinc at protein level, in the nucleus, where cellular zinc sufficiency represses their activity and zinc deficiency is required. In addition, we show that these two transcription factors are functionally redundant to a large extent, and that differential tissue-specific expression patterns might, at least partly, explain distinct regulatory activities. Finally, we show that bZIP24 does not play a central role in the Zn deficiency response. Overall, we provide novel information that advances our understanding of the regulatory activity of bZIP19 and bZIP23.