Dissection of iron signaling and iron accumulation by overexpression of subgroup Ib bHLH039 protein

Micronutrient deficiency-induced oxidative stress in plants

Micronutrients like iron (Fe), zinc (Zn), copper (Cu), manganese (Mn), boron (B), nickel (Ni), and molybdenum (Mo) perform significant roles in the regulation of plant metabolism, growth, and development. Micronutrients, namely Fe, Zn, Cu, Mn, and Ni, are involved in oxidative stress and antioxidant defense as they are cofactors or activators of various antioxidant enzymes, viz., superoxide dismutase (Fe, Cu/Zn, Mn, and Ni), catalase (Fe), and ascorbate peroxidase (Fe). An effort has been made to incorporate recent advances along with classical work done on the micronutrient deficiency-induced oxidative stress and associated antioxidant responses of plants. Deficiency of a micronutrient produces ROS in the cellular compartments. Enzymatic and non-enzymatic antioxidant defense systems are often modulated by micronutrient deficiency to regulate redox balance and scavenge deleterious ROS for the safety of cellular constituents. ROS can strike cellular constituents such as lipids, proteins, and nucleic acids and can destruct cellular membranes and proteins. ROS might act as a signaling molecule and activate the antioxidant proteins by interacting with signaling partners such as respiratory burst oxidase homolog (RBOH), G-proteins, Ca2+, mitogen activated protein kinases (MAPKs), and various transcription factors (TFs). Opinions on probable ROS signaling under micronutrient deficiency have been described in this review. However, further research is required to decipher micronutrient deficiency-induced ROS generation, perception, and associated downstream signaling events, leading to the development of antioxidant responses in plants.

A CYBDOM protein impacts iron homeostasis and primary root growth under phosphate deficiency in Arabidopsis

Arabidopsis primary root growth response to phosphate (Pi) deficiency is mainly controlled by changes in apoplastic iron (Fe). Upon Pi deficiency, apoplastic Fe deposition in the root apical meristem activates pathways leading to the arrest of meristem maintenance and inhibition of cell elongation. Here, we report that a member of the uncharacterized cytochrome b561 and DOMON domain (CYBDOM) protein family, named CRR, promotes iron reduction in an ascorbate-dependent manner and controls apoplastic iron deposition. Under low Pi, the crr mutant shows an enhanced reduction of primary root growth associated with increased apoplastic Fe in the root meristem and a reduction in meristematic cell division. Conversely, CRR overexpression abolishes apoplastic Fe deposition rendering primary root growth insensitive to low Pi. The crr single mutant and crr hyp1 double mutant, harboring a null allele in another member of the CYDOM family, shows increased tolerance to high-Fe stress upon germination and seedling growth. Conversely, CRR overexpression is associated with increased uptake and translocation of Fe to the shoot and results in plants highly sensitive to Fe excess. Our results identify a ferric reductase implicated in Fe homeostasis and developmental responses to abiotic stress, and reveal a biological role for CYBDOM proteins in plants.

Floristic survey, trace element transfers between soil and vegetation and human health risk at an urban industrial wasteland

This study aimed to determine the trace element accumulation in the soil and plants in an industrial wasteland and to estimate the extent of transfer to humans to measure the effects on and risks to vegetation and human health and find bioindicator plants representative of the levels of the main contaminants. In areas with the highest extractable trace element levels, we observed decreases in plant biodiversity explained by the disappearance of several families, favouring the coverage of tolerant species, such as Urtica dioica and Hedera helix. Trace elements were also found in the leaves of several plants, especially in a dominant species that is poorly studied, Alliaria petiolata. Indeed, this species had the highest contents of Zn (1750 mg.kg-1 DW), Ni (13.1 mg.kg-1 DW), and Cd (18 mg.kg-1 DW) found at the site and is a potential Zn bioindicator since its leaf contents were also representative of the Zn extractable contents in soil (R² = 0.94). The hazard quotient and carcinogen risk revealed that most of the site had an identified or possible risk, mainly due to Pb and As. Native species, especially A. petiolata, could be used in phytoextraction to manage and limit these human and environmental risks.

Hordeum vulgare differentiates its response to beneficial bacteria

BACKGROUND

In nature, beneficial bacteria triggering induced systemic resistance (ISR) may protect plants from potential diseases, reducing yield losses caused by diverse pathogens. However, little is known about how the host plant initially responds to different beneficial bacteria. To reveal the impact of different bacteria on barley (Hordeum vulgare), bacterial colonization patterns, gene expression, and composition of seed endophytes were explored.

RESULTS

This study used the soil-borne Ensifer meliloti, as well as Pantoea sp. and Pseudomonas sp. isolated from barley seeds, individually. The results demonstrated that those bacteria persisted in the rhizosphere but with different colonization patterns. Although root-leaf translocation was not observed, all three bacteria induced systemic resistance (ISR) against foliar fungal pathogens. Transcriptome analysis revealed that ion- and stress-related genes were regulated in plants that first encountered bacteria. Iron homeostasis and heat stress responses were involved in the response to E. meliloti and Pantoea sp., even if the iron content was not altered. Heat shock protein-encoding genes responded to inoculation with Pantoea sp. and Pseudomonas sp. Furthermore, bacterial inoculation affected the composition of seed endophytes. Investigation of the following generation indicated that the enhanced resistance was not heritable.

CONCLUSIONS

Here, using barley as a model, we highlighted different responses to three different beneficial bacteria as well as the influence of soil-borne Ensifer meliloti on the seed microbiome. In total, these results can help to understand the interaction between ISR-triggering bacteria and a crop plant, which is essential for the application of biological agents in sustainable agriculture.

Understanding the Mechanisms of Fe Deficiency in the Rhizosphere to Promote Plant Resilience

One of the most significant constraints on agricultural productivity is the low availability of iron (Fe) in soil, which is directly related to biological, physical, and chemical activities in the rhizosphere. The rhizosphere has a high iron requirement due to plant absorption and microorganism density. Plant roots and microbes in the rhizosphere play a significant role in promoting plant iron (Fe) uptake, which impacts plant development and physiology by influencing nutritional, biochemical, and soil components. The concentration of iron accessible to these live organisms in most cultivated soil is quite low due to its solubility being limited by stable oxyhydroxide, hydroxide, and oxides. The dissolution and solubility rates of iron are also significantly affected by soil pH, microbial population, organic matter content, redox processes, and particle size of the soil. In Fe-limiting situations, plants and soil microbes have used active strategies such as acidification, chelation, and reduction, which have an important role to play in enhancing soil iron availability to plants. In response to iron deficiency, plant and soil organisms produce organic (carbohydrates, amino acids, organic acids, phytosiderophores, microbial siderophores, and phenolics) and inorganic (protons) chemicals in the rhizosphere to improve the solubility of poorly accessible Fe pools. The investigation of iron-mediated associations among plants and microorganisms influences plant development and health, providing a distinctive prospect to further our understanding of rhizosphere ecology and iron dynamics. This review clarifies current knowledge of the intricate dynamics of iron with the end goal of presenting an overview of the rhizosphere mechanisms that are involved in the uptake of iron by plants and microorganisms.

SEC14-GOLD protein PATELLIN2 binds IRON-REGULATED TRANSPORTER1 linking root iron uptake to vitamin E

Organisms require micronutrients, and Arabidopsis (Arabidopsis thaliana) IRON-REGULATED TRANSPORTER1 (IRT1) is essential for iron (Fe2+) acquisition into root cells. Uptake of reactive Fe2+ exposes cells to the risk of membrane lipid peroxidation. Surprisingly little is known about how this is avoided. IRT1 activity is controlled by an intracellular variable region (IRT1vr) that acts as a regulatory protein interaction platform. Here, we describe that IRT1vr interacted with peripheral plasma membrane SEC14-Golgi dynamics (SEC14-GOLD) protein PATELLIN2 (PATL2). SEC14 proteins bind lipophilic substrates and transport or present them at the membrane. To date, no direct roles have been attributed to SEC14 proteins in Fe import. PATL2 affected root Fe acquisition responses, interacted with ROS response proteins in roots, and alleviated root lipid peroxidation. PATL2 had high affinity in vitro for the major lipophilic antioxidant vitamin E compound α-tocopherol. Molecular dynamics simulations provided insight into energetic constraints and the orientation and stability of the PATL2-ligand interaction in atomic detail. Hence, this work highlights a compelling mechanism connecting vitamin E with root metal ion transport at the plasma membrane with the participation of an IRT1-interacting and α-tocopherol-binding SEC14 protein.

CAN OF SPINACH, a novel long non-coding RNA, affects iron deficiency responses in Arabidopsis thaliana

Long non-coding RNAs (lncRNAs) are RNA molecules with functions independent of any protein-coding potential. A whole transcriptome (RNA-seq) study of Arabidopsis shoots under iron sufficient and deficient conditions was carried out to determine the genes that are iron-regulated in the shoots. We identified two previously unannotated transcripts on chromosome 1 that are significantly iron-regulated. We have called this iron-regulated lncRNA, CAN OF SPINACH (COS). cos mutants have altered iron levels in leaves and seeds. Despite the low iron levels in the leaves, cos mutants have higher chlorophyll levels than WT plants. Moreover, cos mutants have abnormal development during iron deficiency. Roots of cos mutants are longer than those of WT plants, when grown on iron deficient medium. In addition, cos mutant plants accumulate singlet oxygen during iron deficiency. The mechanism through which COS affects iron deficiency responses is unclear, but small regions of sequence similarity to several genes involved in iron deficiency responses occur in COS, and small RNAs from these regions have been detected. We hypothesize that COS is required for normal adaptation to iron deficiency conditions.

Iron uptake, signaling, and sensing in plants

Iron (Fe) is an essential micronutrient that affects the growth and development of plants because it participates as a cofactor in numerous physiological and biochemical reactions. As a transition metal, Fe is redox active. Fe often exists in soil in the form of insoluble ferric hydroxides that are not bioavailable to plants. Plants have developed sophisticated mechanisms to ensure an adequate supply of Fe in a fluctuating environment. Plants can sense Fe status and modulate the transcription of Fe uptake-associated genes, finally controlling Fe uptake from soil to root. There is a critical need to understand the molecular mechanisms by which plants maintain Fe homeostasis in response to Fe fluctuations. This review focuses on recent advances in elucidating the functions of Fe signaling components. Taking Arabidopsis thaliana and Oryza sativa as examples, this review begins by discussing the Fe acquisition systems that control Fe uptake from soil, the major components that regulate Fe uptake systems, and the perception of Fe status. Future explorations of Fe signal transduction will pave the way for understanding the regulatory mechanisms that underlie the maintenance of plant Fe homeostasis.

Strategies and Bottlenecks in Hexaploid Wheat to Mobilize Soil Iron to Grains

Our knowledge of iron (Fe) uptake and mobilization in plants is mainly based on Arabidopsis and rice. Although multiple players of Fe homeostasis have been elucidated, there is a significant gap in our understanding of crop species, such as wheat. It is, therefore, imperative not only to understand the different hurdles for Fe enrichment in tissues but also to address specifically the knowns/unknowns involved in the plausible mechanism of Fe sensing, signaling, transport, and subsequent storage in plants. In the present review, a unique perspective has been described in light of recent knowledge generated in wheat, an economically important crop. The strategies to boost efficient Fe uptake, transcriptional regulation, and long-distance mobilization in grains have been discussed, emphasizing recent biotechnological routes to load Fe in grains. This article also highlights the new elements of physiological and molecular genetics that underpin the mechanistic insight for the identified Fe-related genes and discusses the bottlenecks in unloading the Fe in grains. The information presented here will provide much-needed resources and directions to overcome challenges and design efficient strategies to enhance the Fe density in wheat grains.

Transcriptome Analysis Revealed the Molecular Response Mechanism of Non-heading Chinese Cabbage to Iron Deficiency Stress

Iron is a trace metal that is found in animals, plants, and the human body. Human iron absorption is hampered by plant iron shortage, which leads to anemia. Leafy vegetables are one of the most direct and efficient sources of iron for humans. Despite the fact that ferrotrophic disorder is common in calcareous soil, however, non-heading Chinese cabbage performs a series of reactions in response to iron deficiency stress that help to preserve iron homeostasis in vivo. In this study, we discovered that iron deficiency stress caused leaf yellowing and impeded plant development in both iron-deficient and control treatments by viewing or measuring phenotypic, chlorophyll content, and Fe²⁺ content in both iron-deficient and control treatments. We found a total of 9213 differentially expressed genes (DEGs) in non-heading Chinese cabbage by comparing root and leaf transcriptome data with iron deficiency and control treatments. For instance, 1927 DEGs co-expressed in root and leaf, including 897 up-regulated and 1030 down-regulated genes, respectively. We selected some key antioxidant genes, hormone signal transduction, iron absorption and transport, chlorophyll metabolism, and transcription factors involved in the regulation of iron deficiency stress utilizing GO enrichment, KEGG enrichment, multiple types of functional annotation, and Weighted Gene Co-expression Network Analysis (WGCNA). This study identifies prospective genes for maintaining iron homeostasis under iron-deficient stress, offering a theoretical foundation for further research into the molecular mechanisms of greater adaptation to iron-deficient stress, and perhaps guiding the development of iron-tolerant varieties.

Long-term acclimation to cadmium exposure reveals extensive phenotypic plasticity in Chlamydomonas

Increasing industrial and anthropogenic activities are producing and releasing more and more pollutants in the environment. Among them, toxic metals are one of the major threats for human health and natural ecosystems. Because photosynthetic organisms play a critical role in primary productivity and pollution management, investigating their response to metal toxicity is of major interest. Here, the green microalga Chlamydomonas (Chlamydomonas reinhardtii) was subjected to short (3 d) or chronic (6 months) exposure to 50 µM cadmium (Cd), and the recovery from chronic exposure was also examined. An extensive phenotypic characterization and transcriptomic analysis showed that the impact of Cd on biomass production of short-term (ST) exposed cells was almost entirely abolished by long-term (LT) acclimation. The underlying mechanisms were initiated at ST and further amplified after LT exposure resulting in a reversible equilibrium allowing biomass production similar to control condition. This included modification of cell wall-related gene expression and biofilm-like structure formation, dynamics of metal ion uptake and homeostasis, photosynthesis efficiency recovery and Cd acclimation through metal homeostasis adjustment. The contribution of the identified coordination of phosphorus and iron homeostasis (partly) mediated by the main phosphorus homeostasis regulator, Phosphate Starvation Response 1, and a basic Helix-Loop-Helix transcription factor (Cre05.g241636) was further investigated. The study reveals the highly dynamic physiological plasticity enabling algal cell growth in an extreme environment.

Interconnection of iron and osmotic stress signalling in plants: is FIT a regulatory hub to cross-connect abscisic acid responses?

Osmotic stresses, such as salinity and drought, have deleterious effects on uptake and translocation of essential mineral nutrients. Iron (Fe) is an important micronutrient that regulates many processes in plants. Plants have adopted various molecular and physiological strategies for Fe acquisition from soil and transport to and within plants. Dynamic Fe signalling in plants tightly regulates Fe uptake and homeostasis. In this way, Fe nutrition is adjusted to growth and stress conditions, and Fe deficiency-regulated transcription factors, such as FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), act as regulatory hubs in these responses. Here, we review and analyse expression of the various components of the Fe signalling during osmotic stresses. We discuss common players in the Fe and osmotic stress signalling. Furthermore, this review focuses on exploring a novel and exciting direct connection of regulatory mechanisms of Fe intake and acquisition with ABA-mediated environmental stress cues, like salt/drought. We propose a model that discuss how environmental stress affects Fe uptake and acquisition and vice versa at molecular-physiological levels in plants.

IRONing out stress problems in crops: a homeostatic perspective

Iron (Fe) is essential for plant growth and therefore plays a key role in influencing crop productivity worldwide. Apart from its central role in chlorophyll biosynthesis and oxidative phosphorylation (electron transfer), it is an important constituent of many enzymes involved in primary metabolism. Fe has different accessibilities to the roots in the rhizosphere depending upon whether it is ferrous (soluble) or ferric (insoluble) oxidation stages, which in turn, determine two kinds of Fe uptake strategies employed by the plants. The reduction strategy is exclusively found in non-graminaceous plants wherein the ferrous Fe²⁺ is absorbed and translocated from the soil through specialized transporters. In contrast, the chelation strategy (widespread in graminaceous plants) relies on the formation of Fe (III)-chelate complex as the necessary requirement of Fe uptake. Once inside the cell, Fe is translocated, compartmentalized and stored through a common set of physiological processes involving many transporters and enzymes whose functions are controlled by underlying genetic components, so that a fine balance of Fe homeostasis is maintained. Recently, molecular and mechanistic aspects of the process involving the role of transcription factors, signaling components, and cis-acting elements have been obtained, which has enabled a much better understanding of its ecophysiology. This mini-review summarizes recent developments in our understanding of Fe transport in higher plants with particular emphasis on crops in the context of major agronomically important abiotic stresses. It also highlights outstanding questions on the regulation of Fe homeostasis and lists potentially useful genes/regulatory pathways that may be useful for subsequent crop improvement under the stresses discussed through either conventional or transgenic approaches.

All together now: regulation of the iron deficiency response

Iron (Fe) is one of the essential micronutrients required by both plants and animals. In humans, Fe deficiency causes anemia, the most prevalent nutritional disorder. Most people rely on plant-based foods as their major Fe source, but plants are a poor source of dietary Fe. Therefore, there is a critical need to better understand the mechanisms involved in the uptake and trafficking of Fe and how plants adapt to Fe deficiency. Fe participates in key cellular functions such as photosynthesis and respiration. Perturbations of Fe uptake, transport, or storage affect plant growth as well as crop yield and plant product quality. Excess Fe has toxic effects due to its high redox activity. Plants, therefore, tightly regulate Fe uptake, distribution, and allocation. Here, we review the regulatory mechanisms involved at the transcriptional and post-translational levels that are critical to prevent Fe uptake except when plants experience Fe deficiency. We discuss the key regulatory network of basic helix-loop-helix (bHLH) transcription factors, including FIT, subgroup Ib, subgroup IVc, and URI (bHLH121), crucial for regulating Fe uptake in Arabidopsis thaliana. Furthermore, we describe the regulators of these transcription factors that either activate or inhibit their function, ensuring optimal Fe uptake that is essential for plant growth.

Reactive oxygen species coordinate the transcriptional responses to iron availability in Arabidopsis

Reactive oxygen species play a central role in the regulation of plant responses to environmental stress. Under prolonged iron (Fe) deficiency, increased levels of hydrogen peroxide (H2O2) initiate signaling events, resulting in the attenuation of Fe acquisition through the inhibition of FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT). As this H2O2 increase occurs in a FIT-dependent manner, our aim was to understand the processes involved in maintaining H2O2 levels under prolonged Fe deficiency and the role of FIT. We identified the CAT2 gene, encoding one of the three Arabidopsis catalase isoforms, as regulated by FIT. CAT2 loss-of-function plants displayed severe susceptibility to Fe deficiency and greatly increased H2O2 levels in roots. Analysis of the Fe homeostasis transcription cascade revealed that H2O2 influences the gene expression of downstream regulators FIT, BHLH genes of group Ib, and POPEYE (PYE); however, H2O2 did not affect their upstream regulators, such as BHLH104 and ILR3. Our data shows that FIT and CAT2 participate in a regulatory loop between H2O2 and prolonged Fe deficiency.

The Emerging Role of GSNOR in Oxidative Stress Regulation

Oxidative stress is a common event in aerobic organisms and a fundamental and unavoidable cost of the aerobic lifestyle. Reactive oxygen and nitrogen species (ROS/RNS) and iron (Fe) are the most common agents that trigger oxidative stress. A conserved enzyme in the S-nitrosoglutathione (GSNO) metabolism, GSNO reductase (GSNOR), modulates a multitude of abiotic and biotic stress responses. In this review, we focus on the emerging role of GSNOR as a master regulator in oxidative stress through its regulation of the interaction of ROS, RNS, and Fe, and highlight recent discoveries in post-translational modifications of GSNOR and functional variations of natural GSNOR variants during oxidative stress. Recent advances in understanding GSNOR regulation show promise for the modulation of oxidative stress in plants.

Transcriptomics Reveals Fast Changes in Salicylate and Jasmonate Signaling Pathways in Shoots of Carbonate-Tolerant Arabidopsis thaliana under Bicarbonate Exposure

High bicarbonate concentrations of calcareous soils with high pH can affect crop performance due to different constraints. Among these, Fe deficiency has mostly been studied. The ability to mobilize sparingly soluble Fe is a key factor for tolerance. Here, a comparative transcriptomic analysis was performed with two naturally selected Arabidopsis thaliana demes, the carbonate-tolerant A1(c+) and the sensitive T6(c-). Analyses of plants exposed to either pH stress alone (pH 5.9 vs. pH 8.3) or to alkalinity caused by 10 mM NaHCO3 (pH 8.3) confirmed better growth and nutrient homeostasis of A1(c+) under alkaline conditions. RNA-sequencing (RNA-seq) revealed that bicarbonate quickly (3 h) induced Fe deficiency-related genes in T6(c-) leaves. Contrastingly, in A1(c+), initial changes concerned receptor-like proteins (RLP), jasmonate (JA) and salicylate (SA) pathways, methionine-derived glucosinolates (GS), sulfur starvation, starch degradation, and cell cycle. Our results suggest that leaves of carbonate-tolerant plants do not sense iron deficiency as fast as sensitive ones. This is in line with a more efficient Fe translocation to aerial parts. In A1(c+) leaves, the activation of other genes related to stress perception, signal transduction, GS, sulfur acquisition, and cell cycle precedes the induction of iron homeostasis mechanisms yielding an efficient response to bicarbonate stress.

Chelators of iron and their role in plant's iron management

Proper transport of metal and their homeostasis is very crucial for the growth and development of plants. Plants root are the primary organs which comes in contact with the stress and thus few modifications occurs, often determining the nutrient efficiency or sometimes as a stress tolerance mechanism. Plant utilizes two strategies for the uptake of iron viz, strategy I-reduction based and strategy II-chelation based. In this review we attempted for a better understanding of how the chelators acts in the mechanism of iron uptake from soils to plants and how iron is distributed in the plants.

Optogenetic control of gene expression in plants in the presence of ambient white light

Optogenetics is the genetic approach for controlling cellular processes with light. It provides spatiotemporal, quantitative and reversible control over biological signaling and metabolic processes, overcoming limitations of chemically inducible systems. However, optogenetics lags in plant research because ambient light required for growth leads to undesired system activation. We solved this issue by developing plant usable light-switch elements (PULSE), an optogenetic tool for reversibly controlling gene expression in plants under ambient light. PULSE combines a blue-light-regulated repressor with a red-light-inducible switch. Gene expression is only activated under red light and remains inactive under white light or in darkness. Supported by a quantitative mathematical model, we characterized PULSE in protoplasts and achieved high induction rates, and we combined it with CRISPR-Cas9-based technologies to target synthetic signaling and developmental pathways. We applied PULSE to control immune responses in plant leaves and generated Arabidopsis transgenic plants. PULSE opens broad experimental avenues in plant research and biotechnology.

The dual benefit of a dominant mutation in Arabidopsis IRON DEFICIENCY TOLERANT1 for iron biofortification and heavy metal phytoremediation

One of the goals of biofortification is to generate iron-enriched crops to combat growth and developmental defects especially iron (Fe) deficiency anaemia. Fe-fortification of food is challenging because soluble Fe is unstable and insoluble Fe is nonbioavailable. Genetic engineering is an alternative approach for Fe-biofortification, but so far strategies to increase Fe content have only encompassed a few genes with limited success. In this study, we demonstrate that the ethyl methanesulfonate (EMS) mutant, iron deficiency tolerant1 (idt1), can accumulate 4-7 times higher amounts of Fe than the wild type in roots, shoots and seeds, and exhibits the metal tolerance and iron accumulation (Metina) phenotype in Arabidopsis. Fe-regulated protein stability and nuclear localisation of the upstream transcriptional regulator bHLH34 were uncovered. The C to T transition mutation resulting in substitution of alanine to valine at amino acid position 320 of bHLH34 (designated as IDT1_A320V ) in a conserved motif among mono- and dicots was found to be responsible for a dominant phenotype that possesses constitutive activation of the Fe regulatory pathway. Overexpression of IDT1_A320V in Arabidopsis and tobacco led to the Metina phenotype; a phenotype that has escalated specificity towards optimising Fe homeostasis and may be useful in Fe-biofortification. Knowledge of the high tolerance and accumulation of heavy metals of this mutant can aid the development of tools for phytoremediation of contaminants.

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.

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.

The PAP/SAL1 retrograde signaling pathway is involved in iron homeostasis

There is a link between PAP/SAL retrograde pathway, ethylene signaling and Fe metabolism in Arabidopsis. Nuclear gene expression is regulated by a diversity of retrograde signals that travel from organelles to the nucleus in a lineal or classical model. One such signal molecule is 3'-phosphoadenisine-5'-phosphate (PAP) and it's in vivo levels are regulated by SAL1/FRY1, a phosphatase enzyme located in chloroplast and mitochondria. This metabolite inhibits the action of a group of exorribonucleases which participate in post-transcriptional gene expression regulation. Transcriptome analysis of Arabidopsis thaliana mutant plants in PAP-SAL1 pathway revealed that the ferritin genes AtFER1, AtFER3, and AtFER4 are up-regulated. In this work we studied Fe metabolism in three different mutants of the PAP/SAL1 retrograde pathway. Mutant plants showed increased Fe accumulation in roots, shoots and seeds when grown in Fe-sufficient condition, and a constitutive activation of the Strategy I Fe uptake genes. As a consequence, they grew more vigorously than wild type plants in Fe-deficient medium. However, when mutant plants grown in Fe-deficient conditions were sprayed with Fe in their leaves, they were unable to deactivate root Fe uptake. Ethylene synthesis inhibition revert the constitutive Fe uptake phenotype. We propose that there is a link between PAP/SAL pathway, ethylene signaling and Fe metabolism.

Phospho-mutant activity assays provide evidence for alternative phospho-regulation pathways of the transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR

The key basic helix-loop-helix (bHLH) transcription factor in iron (Fe) uptake, FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), is controlled by multiple signaling pathways, important to adjust Fe acquisition to growth and environmental constraints. FIT protein exists in active and inactive protein pools, and phosphorylation of serine Ser272 in the C-terminus, a regulatory domain of FIT, provides a trigger for FIT activation. Here, we use phospho-mutant activity assays and study phospho-mimicking and phospho-dead mutations of three additional predicted phosphorylation sites, namely at Ser221 and at tyrosines Tyr238 and Tyr278, besides Ser 272. Phospho-mutations at these sites affect FIT activities in yeast, plant, and mammalian cells. The diverse array of cellular phenotypes is seen at the level of cellular localization, nuclear mobility, homodimerization, and dimerization with the FIT-activating partner bHLH039, promoter transactivation, and protein stability. Phospho-mimicking Tyr mutations of FIT disturb fit mutant plant complementation. Taken together, we provide evidence that FIT is activated through Ser and deactivated through Tyr site phosphorylation. We therefore propose that FIT activity is regulated by alternative phosphorylation pathways.

Mobility and localization of the iron deficiency-induced transcription factor bHLH039 change in the presence of FIT

Regulation of iron (Fe) acquisition and homeostasis is critical for plant survival. In Arabidopsis, Fe deficiency-induced bHLH039 forms a complex with the master regulator FIT and activates it to upregulate Fe acquisition genes. FIT is partitioned between cytoplasm and nucleus, whereby active FIT accumulates more in the nucleus than inactive FIT. At the same time, there is so far no information on the subcellular localization of bHLH039 protein and how it is controlled. We report here that the bHLH039 localization pattern changes depending on the presence of FIT in the cell. When expressed in cells lacking FIT, bHLH039 localizes predominantly in the cytoplasm, including cytoplasmic foci in close proximity to the plasma membrane. The presence of FIT enhances the mobility of bHLH039 and redirects the protein toward primarily nuclear localization, abolishing its accumulation in cytoplasmic foci. This FIT-dependent change in localization of bHLH039 found in transient fluorescent protein expression experiments was confirmed in both leaves and roots of Arabidopsis transgenic plants, stably expressing hemagglutinin-tagged bHLH039 in wild-type or fit mutant background. This posttranslational mechanism for intracellular partitioning of Fe-responsive transcription factors suggests a signaling cascade that translates Fe sensing at the plasma membrane to nuclear accumulation of the transcriptional regulators.

The iron deficiency response in Arabidopsis thaliana requires the phosphorylated transcription factor URI

Iron is an essential nutrient for plants, but excess iron is toxic due to its catalytic role in the formation of hydroxyl radicals. Thus, iron uptake is highly regulated and induced only under iron deficiency. The mechanisms of iron uptake in roots are well characterized, but less is known about how plants perceive iron deficiency. We show that a basic helix-loop-helix (bHLH) transcription factor Upstream Regulator of IRT1 (URI) acts as an essential part of the iron deficiency signaling pathway in Arabidopsis thaliana The uri mutant is defective in inducing Iron-Regulated Transporter1 (IRT1) and Ferric Reduction Oxidase2 (FRO2) and their transcriptional regulators FER-like iron deficiency-induced transcription factor (FIT) and bHLH38/39/100/101 in response to iron deficiency. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) reveals direct binding of URI to promoters of many iron-regulated genes, including bHLH38/39/100/101 but not FIT While URI transcript and protein are expressed regardless of iron status, a phosphorylated form of URI only accumulates under iron deficiency. Phosphorylated URI is subject to proteasome-dependent degradation during iron resupply, and turnover of phosphorylated URI is dependent on the E3 ligase BTS. The subgroup IVc bHLH transcription factors, which have previously been shown to regulate bHLH38/39/100/101, coimmunoprecipitate with URI mainly under Fe-deficient conditions, suggesting that it is the phosphorylated form of URI that is capable of forming heterodimers in vivo. We propose that the phosphorylated form of URI accumulates under Fe deficiency, forms heterodimers with subgroup IVc proteins, and induces transcription of bHLH38/39/100/101 These transcription factors in turn heterodimerize with FIT and drive the transcription of IRT1 and FRO2 to increase Fe uptake.

Iron acquisition strategies in land plants: not so different after all

Due to its ability to accept and donate electrons, iron (Fe) is an indispensable component of electron transport chains and a cofactor in many vital enzymes. Except for waterlogged conditions, under which the lack of oxygen prevents oxidation and precipitation of iron as Fe³⁺ hydroxides, the availability of iron in soils is generally far below the plant's demand for optimal growth. Plants have evolved two phylogenetically separated and elaborately regulated strategies to mobilize iron from the soil, featuring mechanisms which are thought to be mutually exclusive. However, recent studies uncovered several shared components of the two strategies, questioning the validity of the concept of mutual exclusivity. Here, we use publicly available data obtained from the model species rice (Oryza sativa) to unveil similarities and incongruities between co-expression networks derived from transcriptomic profiling of iron-deficient rice and Arabidopsis plants. This approach revealed striking similarities in the topographies of the resulting co-expression networks with relatively minor deviations in the molecular attributes of the comprised genes, which nonetheless lead to different physiological functions. The analysis also discovered several novel players that are possibly involved in the regulation plant adaptation to iron deficiency.

New aspects of iron-copper crosstalk uncovered by transcriptomic characterization of Col-0 and the copper uptake mutant spl7 in Arabidopsis thaliana

Iron (Fe) and copper (Cu) are essential micronutrients for energy metabolism and reactive oxygen species (ROS) scavenging. Some Cu-containing proteins can be substituted with Fe-containing proteins, and vice versa, while several Arabidopsis genes are regulated by both metals. Few details of how plants coordinate Fe-Cu crosstalk are known. Gene expression was measured in the roots and rosettes of Fe, Cu, and simultaneously Fe and Cu deficient WT plants and a mutant of the Cu-uptake transcription factor SPL7. The spl7 mutant accumulated excess Fe under normal conditions, and lower Fe supply rescued the growth phenotype and normalized the Fe : Cu ratios. Most Fe regulated genes were expressed similarly in the WT and spl7 mutant, although at higher fold-change levels in spl7 mutants. Expression patterns indicated that both SPL7 and the FIT Fe uptake transcription factor influenced the expression of many key Fe uptake genes. Most notably, the newly discovered IMA/FEP genes and the subgroup Ib bHLH genes, which are upstream of Fe uptake responses, were repressed in the WT under Cu deficiency. Several AP2/ethylene response factor (AP2/ERF) genes and other redox homeostasis network genes were derepressed in spl7 mutants. Together, we present new information about Fe-Cu crosstalk in plants that could be applied for developing abiotic stress tolerant crops.

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.

New insight into the molecular basis of cadmium stress responses of wild paper mulberry plant by transcriptome analysis

BACKGROUND

Heavy metal contamination is becoming a limitation to the utilization of soil and the distribution of vegetation. In particular, cadmium (Cd) pollution has had a serious impact on the food chain. Broussonetia papyrifera is a widely distributed pioneer tree species of heavy metal contaminated areas with important economic value. However, little is known about the genomic background of the Cd-tolerance mechanism in B. papyrifera.

RESULTS

The CdCl₂ responsive physiology was evaluated and proved to be involved in antioxidase activity and active oxygen species (ROS) accumulation. The leaf and root transcriptomes derived from B. papyrifera grown under normal and CdCl₂ stress conditions were systematically investigated using the Illumina HiSeq method. A total of 180,678,660 bp (27.1 GB) clean reads were assembled into 589,487 high-quality unigenes, of which 256,025 (43.43% of the total) and 250,251 (42.45% of the total) were aligned in Gene Ontology (GO) and Protein family (Pfam), respectively. A total of 24,414 differentially expressed genes (DEGs) were GO-annotated into 53, 23, 55, and 60 terms from the transcriptomes of root and leaf tissues under Cd stress and control conditions. A total of 117,547 Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO)-annotated DEGs were enriched in at least 47 KEGG pathway terms among the four comparisons. Many genes encoding important transcription factors (e.g., auxin/indole-3-acetic acid (AUX/IAA), basic helix-loop-helix (bHLH), DNA-binding one zinc finger (Dof), and MYB) and proteins involved in plant-pathogen interactions, phenylpropanoid biosynthesis, plant hormone signal transduction, oxidative phosphorylation, carbon fixation, peroxisomes, flavonoid biosynthesis, and glutathione metabolism, among others, were substantially upregulated under CdCl₂ stress.

CONCLUSIONS

These genes represent important candidates for studying Cd-response mechanisms and molecular biology of B. papyrifera and related species. Our findings provide a genomic sequence resource for functional genetic assignments in B. papyrifera, which will help elucidate the molecular mechanisms of its Cd-stress responses and facilitate the bioremediation of heavy metal contaminated areas via breeding of new stress-tolerant cultivars.

The mitochondrial copper chaperone COX19 influences copper and iron homeostasis in arabidopsis

The mitochondrial metallochaperone COX19 influences iron and copper responses highlighting a role of mitochondria in modulating metal homeostasis in Arabidopsis. The mitochondrial copper chaperone COX19 participates in the biogenesis of cytochrome c oxidase (COX) in yeast and humans. In this work, we studied the function of COX19 in Arabidopsis thaliana, using plants with either decreased or increased COX19 levels. A fusion of COX19 to the red fluorescent protein localized to mitochondria in vivo, suggesting that Arabidopsis COX19 is a mitochondrial protein. Silencing of COX19 using an artificial miRNA did not cause changes in COX activity levels or respiration in plants grown under standard conditions. These amiCOX19 plants, however, showed decreased expression of the low-copper responsive miRNA gene MIR398b and an induction of the miR398 target CSD1 relative to wild-type plants. Plants with increased COX19 levels, instead, showed induction of MIR398b and other low-copper responsive genes. In addition, global transcriptional changes in rosettes of amiCOX19 plants resembled those observed under iron deficiency. Phenotypic analysis indicated that the roots of amiCOX19 plants show altered growth responses to copper excess and iron deficiency. COX activity levels and COX-dependent respiration were lower in amiCOX19 plants than in wild-type plants under iron deficiency conditions, suggesting that COX19 function is particularly important for COX assembly under iron deficiency. The results indicate that the mitochondrial copper chaperone COX19 has a role in regulating copper and iron homeostasis and responses in plants.

The Transcriptional Control of Iron Homeostasis in Plants: A Tale of bHLH Transcription Factors?

Iron is one of the most important micronutrients in plants as it is involved in many cellular functions (e.g., photosynthesis and respiration). Any defect in iron availability will affect plant growth and development as well as crop yield and plant product quality. Thus, iron homeostasis must be tightly controlled in order to ensure optimal absorption of this mineral element. Understanding mechanisms governing iron homeostasis in plants has been the focus of several studies during the past 10 years. These studies have greatly improved our understanding of the mechanisms involved, revealing a sophisticated iron-dependent transcriptional regulatory network. Strikingly, these studies have also highlighted that this regulatory web relies on the activity of numerous transcriptional regulators that belong to the same group of transcription factors (TF), the bHLH (basic helix-loop-helix) family. This is best exemplified in Arabidopsis where, to date, 16 bHLH TF have been characterized as involved in this process and acting in a complex regulatory cascade. Interestingly, among these bHLH TF some form specific clades, indicating that peculiar function dedicated to the maintenance of iron homeostasis, have emerged during the course of the evolution of the green lineage. Within this mini review, we present new insights on the control of iron homeostasis and the involvement of bHLH TF in this metabolic process.

PRC2-Mediated H3K27me3 Contributes to Transcriptional Regulation of FIT-Dependent Iron Deficiency Response

Iron is an essential micronutrient for nearly all organisms, but excessive iron can lead to the formation of cytotoxic reactive oxygen species. Therefore, iron acquisition and homeostasis must be tightly regulated. Plants have evolved complex mechanisms to optimize their use of iron, which is one of the most limiting nutrients in the soil. In particular, transcriptional regulation is vital for regulating iron in plants, and much work has revealed the role of transcription factors on this front. Our study adds novel insights to the transcriptional regulation of iron homeostasis in plants by showing that chromatin remodeling via histone 3 lysine 27 trimethylation (H3K27me3) modulates the expression of FIT-dependent genes under iron deficiency. We provide evidence that FIT-dependent iron acquisition genes, IRT1 and FRO2, as well as FIT itself are direct targets of PRC2-mediated H3K27me3. In the clf mutant, which lacks the predominant H3K27 tri-methyltransferase, induction of FIT, FRO2, IRT1, and other FIT-regulated genes in roots is significantly higher under iron deficient conditions than in wild type. Furthermore, we observe that clf mutants are more tolerant to iron deficiency than wild type, indicating that gene expression levels appear to be limiting the plants ability to access iron. We propose that H3K27me3 attenuates the induction of FIT-target genes under iron deficiency and hypothesize that this may serve as a mechanism to restrict the maximum level of induction of iron acquisition genes to prevent iron overload.

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

Fe and Zn are essential micronutrients for plant growth, and the interrelationship regarding their homeostasis is very complicated. In this study, we identified a FIT-binding protein (FBP) using the yeast two-hybrid system. The C-terminus of FBP binds to the bHLH domain of FIT, abolishing the DNA-binding capacity of FIT. Knockout of FBP results in an enhanced expression of NAS genes and a higher nicotianamine content, and the fbp mutant exhibits tolerance to excessive Zn. Physiological analyses reveal that the mutant fbp retains a larger amount of Zn in roots and transfers a greater proportion of Fe to shoots than that in wild type under Zn-excessive stress. As FBP is expressed in the root stele, the negative regulation caused by sequestration of FIT is restricted to this tissue, whereas other FIT-regulated genes, such as IRT1 and FRO2, which mainly expressed in root epidermis, do not show transcriptional upregulation in the fbp mutant. As an antagonistic partner, FBP offers a new approach to spatially fine-tune the expression of genes controlled by FIT. In conclusion, our findings provide a new insight to understand the interrelationship of Fe and Zn homeostasis in plants.