Role of hormones in the induction of iron deficiency responses in Arabidopsis roots

Rooting for survival: how plants tackle a challenging environment through a diversity of root forms and functions

The current climate crisis has global impacts and will affect the physiology of plants across every continent. Ensuring resilience of our agricultural and natural ecosystems to the environmental stresses imposed by climate change will require molecular insight into the adaptations employed by a diverse array of plants. However, most current studies continue to focus on a limited set of model species or crops. Root systems are particularly understudied even though their functions in water and nutrient uptake are likely pivotal for plant stress resilience and sustainable agriculture. In this review, we highlight anatomical adaptations in roots that enable plant survival in different ecological niches. We then present the current state of knowledge for the molecular underpinnings of these adaptations. Finally, we identify areas where future research using a biodiversity approach can fill knowledge gaps necessary for the development of climate-resilient crops of the future.

Tailoring Core-Shell Metal Coordination for Smart Seed Coatings in Sustainable Agriculture

The international agriculture and food security sector is grappling with challenges like low crop yields, soil health deficiencies, and inefficient agrochemical use. The application of smart nanotechnology in agriculture, particularly surface functionalization, holds promise but has limited implementation. Engineered nanomaterials used as seed treatments, known as nanopriming, offer a simple technology to improve crop yield and stress tolerance. In this study, a multicomponent platform called Phelm (Phenolic network with a lipid core and metal coordinated shell) is proposed for encapsulating a commercial plant growth regulator, indole-3 acetic acid (IAA). Phelm comprises a hydrophobic solid lipid core, loaded with IAA, and an outer metal coordinated phenolic shell of tannic acid (TA) and Fe3+. The platform aims to treat seeds with encapsulated IAA, which can be controllably released, as well as protect the germination process at high salt concentrations. Phelm showed a remarkable increase in growth parameters of wheat seeds up to 58.6%, despite being irrigated with high concentrations of saltwater (100 mM). These findings suggest that nanopriming of seeds can effectively increase their efficacy even under abiotic stress conditions, which can drastically improve crop yields. Moreover, we envisage that the Phelm core/shell assembly can encapsulate a wide range of agrochemicals and biostimulants to promote sustainable and smart agricultural practices.

A multi-omics insight on the interplay between iron deficiency and N forms in tomato

Introduction

Nitrogen (N) and iron (Fe) are involved in several biochemical processes in living organisms, and their limited bioavailability is a strong constraint for plant growth and yield. This work investigated the interplay between Fe and N nutritional pathways in tomato plants kept under N and Fe deficiency and then resupplied with Fe and N (as nitrate, ammonium, or urea) through a physiological, metabolomics and gene expression study.

Results

After 24 hours of Fe resupply, the Fe concentration in Fe-deficient roots was dependent on the applied N form (following the pattern: nitrate > urea > ammonium > Fe-deficient control), and whereas in leaves of urea treated plants the Fe concentration was lower in comparison to the other N forms. Untargeted metabolomics pointed out distinctive modulations of plant metabolism in a treatment-dependent manner. Overall, N-containing metabolites were affected by the treatments in both leaves and roots, while N form significantly shaped the phytohormone profile. Moreover, the simultaneous application of Fe with N to Fe-deficient plants elicited secondary metabolites' accumulation, such as phenylpropanoids, depending on the applied N form (mainly by urea, followed by nitrate and ammonium). After 4 hours of treatment, ammonium- and urea-treated roots showed a reduction of enzymatic activity of Fe(III)-chelate reductase (FCR), compared to nitrate or N-depleted plants (maintained in Fe deficiency, where FCR was maintained at high levels). The response of nitrate-treated plants leads to the improvement of Fe concentration in tomato roots and the increase of Fe(II) transporter (IRT1) gene expression in tomato roots.

Conclusions

Our results strengthen and improve the understanding about the interaction between N and Fe nutritional pathways, thinning the current knowledge gap.

Metabolism of Malus halliana Roots Provides Insights into Iron Deficiency Tolerance Mechanisms

Iron (Fe) deficiency is one of the most common micronutrient imbalances limiting plant growth globally, especially in arid and saline alkali regions due to the decreased availability of Fe in alkaline soils. Malus halliana grows well in arid regions and is tolerant of Fe deficiency. Here, a physiological and metabolomic approach was used to analyze the short-term molecular response of M. halliana roots to Fe deficiency. On the one hand, physiological data show that the root activity first increased and then decreased with the prolongation of the stress time, but the change trend of root pH was just the opposite. The total Fe content decreased gradually, while the effective Fe decreased at 12 h and increased at 3 d. The activity of iron reductase (FCR) increased with the prolongation of stress. On the other hand, a total of 61, 73, and 45 metabolites were identified by GC-MS in three pairs: R12h (Fe deficiency 12 h) vs. R0h (Fe deficiency 0 h), R3d (Fe deficiency 3 d) vs. R0h, and R3d vs. R12h, respectively. Sucrose, as a source of energy, produces monosaccharides such as glucose by hydrolysis, while glucose accumulates significantly at the first (R12h vs. R0h) and third time points (R3d vs. R0h). Carbohydrates (digalacturonate, L-xylitol, ribitol, D-xylulose, glucose, and glycerol) are degraded into pyruvate through glycolysis and pentose phosphate, which participate in the TCA. Glutathione metabolism and the TCA cycle coordinate with each other, actively respond to Fe deficiency stress, and synthesize secondary metabolites at the same time. This study thoroughly examines the metabolite response to plant iron deficiency, highlighting the crucial roles of sugar metabolism, tricarboxylic acid cycle regulation, and glutathione metabolism in the short-term iron deficiency response of apples. It also lays the groundwork for future research on analyzing iron deficiency tolerance.

Soil and Mineral Nutrients in Plant Health: A Prospective Study of Iron and Phosphorus in the Growth and Development of Plants

Plants being sessile are exposed to different environmental challenges and consequent stresses associated with them. With the prerequisite of minerals for growth and development, they coordinate their mobilization from the soil through their roots. Phosphorus (P) and iron (Fe) are macro- and micronutrient; P serves as an important component of biological macromolecules, besides driving major cellular processes, including photosynthesis and respiration, and Fe performs the function as a cofactor for enzymes of vital metabolic pathways. These minerals help in maintaining plant vigor via alterations in the pH, nutrient content, release of exudates at the root surface, changing dynamics of root microbial population, and modulation of the activity of redox enzymes. Despite this, their low solubility and relative immobilization in soil make them inaccessible for utilization by plants. Moreover, plants have evolved distinct mechanisms to cope with these stresses and coregulate the levels of minerals (Fe, P, etc.) toward the maintenance of homeostasis. The present study aims at examining the uptake mechanisms of Fe and P, and their translocation, storage, and role in executing different cellular processes in plants. It also summarizes the toxicological aspects of these minerals in terms of their effects on germination, nutrient uptake, plant-water relationship, and overall yield. Considered as an important and indispensable component of sustainable agriculture, a separate section covers the current knowledge on the cross-talk between Fe and P and integrates complete and balanced information of their effect on plant hormone levels.

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.

Application of green synthesized bimetallic nZVI-Cu nanoparticle as a sustainable alternative to chemical fertilizers to enhance growth and photosynthetic efficiency of rice seedlings

Application of nanomaterials in agriculture has been extensively explored over the past decade leading to a wide ambit of nanoparticle-based agrochemicals. Metallic nanoparticles consisting of plant macro- and micro-nutrients have been used as nutritional supplements for plants through soil amendments, foliar sprays, or seed treatment. However, most of these studies emphasize monometallic nanoparticles which limit the range of usage and effectivity of such nanoparticles (NPs). Hence, we have employed a bimetallic nanoparticle (BNP) consisting of two different micro-nutrients (Cu & Fe) in rice plants to test its efficacy in terms of growth and photosynthesis. Several experiments were designed to assess growth (root-shoot length, relative water content) and photosynthetic parameters (pigment content, relative expression of rbcS, rbcL & ChlGetc.). To determine whether the treatment induced any oxidative stress or structural anomalies within the plant cells, histochemical staining, anti-oxidant enzyme activities, FTIR, and SEM micrographs were undertaken. Results indicated that foliar application of 5 mg L-1 BNP increased vigor and photosynthetic efficiency whereas 10 mg L-1 concentration induced oxidative stress to some extent. Furthermore, the BNP treatment did not perturb the structural integrity of the exposed plant parts and also did not induce any cytotoxicity. Application of BNPs in agriculture has not been explored extensively to date and this study is one of the first reports that not only documents the effectivity of Cu-Fe BNP but also critically explores the safety of its usage on rice plants making it a useful lead to design new BNPs and explore their efficacy.

Nitric Oxide and Globin Glb1 Regulate Fusarium oxysporum Infection of Arabidopsis thaliana

Plants continuously interact with fungi, some of which, such as Fusarium oxysporum, are lethal, leading to reduced crop yields. Recently, nitric oxide (NO) has been found to play a regulatory role in plant responses to F. oxysporum, although the underlying mechanisms involved are poorly understood. In this study, we show that Arabidopsis mutants with altered levels of phytoglobin 1 (Glb1) have a higher survival rate than wild type (WT) after infection with F. oxysporum, although all the genotypes analyzed exhibited a similar fungal burden. None of the defense responses that were analyzed in Glb1 lines, such as phenols, iron metabolism, peroxidase activity, or reactive oxygen species (ROS) production, appear to explain their higher survival rates. However, the early induction of the PR genes may be one of the reasons for the observed survival rate of Glb1 lines infected with F. oxysporum. Furthermore, while PR1 expression was induced in Glb1 lines very early on the response to F. oxysporum, this induction was not observed in WT plants.

Cell type-specific mapping of ion distribution in Arabidopsis thaliana roots

Cell type-specific mapping of element distribution is critical to fully understand how roots partition nutrients and toxic elements with aboveground parts. In this study, we developed a method that combines fluorescence-activated cell sorting (FACS) with inductively coupled plasma mass spectrometry (ICP-MS) to assess the ionome of different cell populations within Arabidopsis thaliana roots. The method reveals that most elements exhibit a radial concentration gradient increasing from the rhizodermis to inner cell layers, and detected previously unknown ionomic changes resulting from perturbed xylem loading processes. With this approach, we also identify a strong accumulation of manganese in trichoblasts of iron-deficient roots. We demonstrate that confining manganese sequestration in trichoblasts but not in endodermal cells efficiently retains manganese in roots, therefore preventing toxicity in shoots. These results indicate the existence of cell type-specific constraints for efficient metal sequestration in roots. Thus, our approach opens an avenue to investigate element compartmentation and transport pathways in plants.

The evolution of plant proton pump regulation via the R domain may have facilitated plant terrestrialization

Plasma membrane (PM) H⁺-ATPases are the electrogenic proton pumps that export H⁺ from plant and fungal cells to acidify the surroundings and generate a membrane potential. Plant PM H⁺-ATPases are equipped with a C‑terminal autoinhibitory regulatory (R) domain of about 100 amino acid residues, which could not be identified in the PM H⁺-ATPases of green algae but appeared fully developed in immediate streptophyte algal predecessors of land plants. To explore the physiological significance of this domain, we created in vivo C-terminal truncations of autoinhibited PM H⁺‑ATPase2 (AHA2), one of the two major isoforms in the land plant Arabidopsis thaliana. As more residues were deleted, the mutant plants became progressively more efficient in proton extrusion, concomitant with increased expansion growth and nutrient uptake. However, as the hyperactivated AHA2 also contributed to stomatal pore opening, which provides an exit pathway for water and an entrance pathway for pests, the mutant plants were more susceptible to biotic and abiotic stresses, pathogen invasion and water loss, respectively. Taken together, our results demonstrate that pump regulation through the R domain is crucial for land plant fitness and by controlling growth and nutrient uptake might have been necessary already for the successful water-to-land transition of plants.

Identification of iron and zinc responsive genes in pearl millet using genome-wide RNA-sequencing approach

Pearl millet (Pennisetum glaucum L.), an important source of iron (Fe) and zinc (Zn) for millions of families in dryland tropics, helps in eradicating micronutrient malnutrition. The crop is rich in Fe and Zn, therefore, identification of the key genes operating the mineral pathways is an important step to accelerate the development of biofortified cultivars. In a first-of-its-kind experiment, leaf and root samples of a pearl millet inbred ICMB 1505 were exposed to combinations of Fe and Zn stress conditions using the hydroponics method, and a whole-genome transcriptome assay was carried out to characterize the differentially expressed genes (DEGs) and pathways. A total of 37,093 DEGs under different combinations of stress conditions were identified, of which, 7,023 and 9,996 DEGs were reported in the leaf and root stress treatments, respectively. Among the 10,194 unique DEGs, 8,605 were annotated to cellular, biological, and molecular functions and 458 DEGs were assigned to 39 pathways. The results revealed the expression of major genes related to the mugineic acid pathway, phytohormones, chlorophyll biosynthesis, photosynthesis, and carbohydrate metabolism during Fe and Zn stress. The cross-talks between the Fe and Zn provided information on their dual and opposite regulation of key uptake and transporter genes under Fe and Zn deficiency. SNP haplotypes in rice, maize, sorghum, and foxtail millet as well as in Arabidopsis using pearl millet Fe and Zn responsive genes could be used for designing the markers in staple crops. Our results will assist in developing Fe and Zn-efficient pearl millet varieties in biofortification breeding programs and precision delivery mechanisms to ameliorate malnutrition in South Asia and Sub-Saharan Africa.

MbHY5-MbYSL7 mediates chlorophyll synthesis and iron transport under iron deficiency in Malus baccata

Iron (Fe) plays an important role in cellular respiration and catalytic reactions of metalloproteins in plants and animals. Plants maintain iron homeostasis through absorption, translocation, storage, and compartmentalization of iron via a cooperative regulative network. Here, we showed different physiological characteristics in the leaves and roots of Malus baccata under Fe sufficiency and Fe deficiency conditions and propose that MbHY5 (elongated hypocotyl 5), an important transcription factor for its function in photomorphogenesis, participated in Fe deficiency response in both the leaves and roots of M. baccata. The gene co-expression network showed that MbHY5 was involved in the regulation of chlorophyll synthesis and Fe transport pathway under Fe-limiting conditions. Specifically, we found that Fe deficiency induced the expression of MbYSL7 in root, which was positively regulated by MbHY5. Overexpressing or silencing MbYSL7 influenced the expression of MbHY5 in M. baccata.

Overexpression of Nicotianamine Synthase (AtNAS1) Increases Iron Accumulation in the Tuber of Potato

Iron (Fe) deficiency is a global health problem, especially in underdeveloped countries. Biofortification with genetic engineering methods has been used to improve Fe nutrition in a number of crops. Various steps, e.g., uptake, distribution, and storage, involved in Fe homeostasis have been manipulated to increase the Fe concentration in the edible portions of plants. Nicotianamine (NA) is an important metal ion chelator in plants. It promotes the mobility of Fe and decreases cellular Fe toxicity. Increasing the Fe content in crops by promoting NA synthesis could help decrease human diseases associated with Fe deficiency. In the present study, Arabidopsis thaliana nicotianamine synthase 1 (AtNAS1) was overexpressed in potato (Solanum tuberosum, St) under the control of the cauliflower mosaic virus 35S promoter. Transgenic plants had a significantly increased amount of Fe in tubers (52.7 µg/g dry weight, 2.4-fold the amount in wild-type tubers), while no differences in plant phenotype or yield were detected between transgenic and wild-type plants. The expression of genes involved in root mineral uptake and homeostasis, such as StYSL1, StIRT1, StFRO1, and StNAS, was also altered in the roots and leaves of the transgenic plants. Our results demonstrate that the manipulation of Fe chelation is a useful strategy for Fe nutrition improvement, and the increased Fe accumulation in tubers of transgenic potato plants is most likely caused by the increased movement of Fe from the leaf to the tuber.

Trihelix transcription factors GTL1 and DF1 prevent aberrant root hair formation in an excess nutrient condition

Root hair growth is tuned in response to the environment surrounding plants. While most previous studies focused on the enhancement of root hair growth during nutrient starvation, few studies investigated the root hair response in the presence of excess nutrients. We report that the post-embryonic growth of wild-type Arabidopsis plants is strongly suppressed with increasing nutrient availability, particularly in the case of root hair growth. We further used gene expression profiling to analyze how excess nutrient availability affects root hair growth, and found that RHD6 subfamily genes, which are positive regulators of root hair growth, are downregulated in this condition. However, defects in GTL1 and DF1, which are negative regulators of root hair growth, cause frail and swollen root hairs to form when excess nutrients are supplied. Additionally, we observed that the RHD6 subfamily genes are mis-expressed in gtl1-1 df1-1. Furthermore, overexpression of RSL4, an RHD6 subfamily gene, induces swollen root hairs in the face of a nutrient overload, while mutation of RSL4 in gtl1-1 df1-1 restore root hair swelling phenotype. In conclusion, our data suggest that GTL1 and DF1 prevent unnecessary root hair formation by repressing RSL4 under excess nutrient conditions.

From leaves to roots: Biophysical models of transport of substances in plants

The transport processes of substances in various plant tissues are extremely diverse. However, models aimed at elucidating the mechanisms of such processes are almost absent in the literature. A unified view of all these transport processes is necessary, considering the laws of statistical physics and thermodynamics. A model of active ion transport was constructed based on the laws of statistical physics. Using this model, we traced the entire pathway of substances and energy in a plant. The pathway included aspects of the production of energy in the process of photosynthesis, consumption of energy to obtain nutrients from the soil, transport of such substances to the main organelles of all types of plant cells, the rise of water with dissolved substances along the trunk to the leaves, and the evaporation of water, accompanied by a change in the percentage of isotopes caused by different rates of evaporation. Models of ion transport in the chloroplasts and mitochondria of plant cells have been constructed. A generalized model comprising plant cells and their vacuoles was analyzed. A model of the transport of substances in the roots of plants was also developed. Based on this model, the problem of transport of substances in tall trees has been considered. The calculated concentrations of ions in the vacuoles of cells and resting potentials agreed well with the experimental data.

Root hair growth from the pH point of view

Root hairs are tubular outgrowths of epidermal cells that increase the root surface area and thereby make the root more efficient at absorbing water and nutrients. Their expansion is limited to the root hair apex, where growth is reported to take place in a pulsating manner. These growth pulses coincide with oscillations of the apoplastic and cytosolic pH in a similar way as has been reported for pollen tubes. Likewise, the concentrations of apoplastic reactive oxygen species (ROS) and cytoplasmic Ca²⁺ oscillate with the same periodicity as growth. Whereas ROS appear to control cell wall extensibility and opening of Ca²⁺ channels, the role of protons as a growth signal in root hairs is less clear and may differ from that in pollen tubes where plasma membrane H⁺-ATPases have been shown to sustain growth. In this review, we outline our current understanding of how pH contributes to root hair development.

Comparative physiological, biochemical and transcriptomic analysis of hexaploid wheat (T. aestivum L.) roots and shoots identifies potential pathways and their molecular regulatory network during Fe and Zn starvation

The combined effect of iron (Fe) and zinc (Zn) starvation on their uptake and transportation and the molecular regulatory networks is poorly understood in wheat. To fill this gap, we performed a comprehensive physiological, biochemical and transcriptome analysis in two bread wheat genotypes, i.e. Narmada 195 and PBW 502, differing in inherent Fe and Zn content. Compared to PBW 502, Narmada 195 exhibited increased tolerance to Fe and Zn withdrawal by significantly modulating the critical physiological and biochemical parameters. We identified 25 core genes associated with four key pathways, i.e. methionine cycle, phytosiderophore biosynthesis, antioxidant and transport system, that exhibited significant up-regulation in both the genotypes with a maximum in Narmada 195. We also identified 26 microRNAs targeting 14 core genes across the four pathways. Together, core genes identified can serve as valuable resources for further functional research for genetic improvement of Fe and Zn content in wheat grain.

Root Silicon Addition Induces Fe Deficiency in Cucumber Plants, but Facilitates Their Recovery After Fe Resupply. A Comparison With Si Foliar Sprays

Silicon has not been cataloged as an essential element for higher plants. However, it has shown beneficial effects on many crops, especially under abiotic and biotic stresses. Silicon fertilization was evaluated for the first time on plants exposed to fluctuations in an Fe regime (Fe sufficiency followed by Fe deficiency and, in turn, by Fe resupply). Root and foliar Si applications were compared using cucumber plants that were hydroponically grown in a growth chamber under different Fe nutritional statuses and Si applied either to the roots or to the shoots. The SPAD index, Fe, and Mn concentration, ROS, total phenolic compounds, MDA concentration, phytohormone balance, and cell cycle were determined. The results obtained showed that the addition of Si to the roots induced an Fe shortage in plants grown under optimal or deficient Fe nutritional conditions, but this was not observed when Si was applied to the leaves. Plant recovery following Fe resupply was more effective in the Si-treated plants than in the untreated plants. A relationship between the ROS concentration, hormonal balance, and cell cycle under different Fe regimes and in the presence or absence of Si was also studied. The contribution of Si to this signaling pathway appears to be related more to the induction of Fe deficiency, than to any direct biochemical or metabolic processes. However, these roles could not be completely ruled out because several hormone differences could only be explained by the addition of Si.

Computational solutions for modeling and controlling plant response to abiotic stresses: a review with focus on iron deficiency

Computational solutions enable plant scientists to model protein-mediated stress responses and characterize novel gene functions that coordinate responses to a variety of abiotic stress conditions. Recently, density functional theory was used to study proteins active sites and elucidate enzyme conversion mechanisms involved in iron deficiency responsive signaling pathways. Computational approaches for protein homology modeling and the kinetic modeling of signaling pathways have also resolved the identity and function in proteins involved in iron deficiency signaling pathways. Significant changes in gene relationships under other stress conditions, such as heat or drought stress, have been recently identified using differential network analysis, suggesting that stress tolerance is achieved through asynchronous control. Moreover, the increasing development and use of statistical modeling and systematic modeling of transcriptomic data have provided significant insight into the gene regulatory mechanisms associated with abiotic stress responses. These types of in silico approaches have facilitated the plant science community's future goals of developing multi-scale models of responses to iron deficiency stress and other abiotic stress conditions.

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.

Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots

Plant iron deficiency (-Fe) activates a complex regulatory network that coordinates root Fe uptake and distribution to sink tissues. In Arabidopsis (Arabidopsis thaliana), FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), a basic helix-loop-helix (bHLH) transcription factor (TF), regulates root Fe acquisition genes. Many other -Fe-induced genes are FIT independent, and instead regulated by other bHLH TFs and by yet unknown TFs. The cis-regulatory code, that is, the cis-regulatory elements (CREs) and their combinations that regulate plant -Fe-responses, remains largely elusive. Using Arabidopsis root transcriptome data and coexpression clustering, we identified over 100 putative CREs (pCREs) that predicted -Fe-induced gene expression in computational models. To assess pCRE properties and possible functions, we used large-scale in vitro TF binding data, positional bias, and evolutionary conservation. As one example, our approach uncovered pCREs resembling IDE1 (iron deficiency-responsive element 1), a known grass -Fe response CRE. Arabidopsis IDE1-likes were associated with FIT-dependent gene expression, more specifically with biosynthesis of Fe-chelating compounds. Thus, IDE1 seems to be conserved in grass and nongrass species. Our pCREs matched among others in vitro binding sites of B3, NAC, bZIP, and TCP TFs, which might be regulators of -Fe responses. Altogether, our findings provide a comprehensive source of cis-regulatory information for -Fe-responsive genes that advance our mechanistic understanding and inform future efforts in engineering plants with more efficient Fe uptake or transport systems.

Modulatory Role of Reactive Oxygen Species in Root Development in Model Plant of Arabidopsis thaliana

Reactive oxygen species (ROS), a type of oxygen monoelectronic reduction product, have a higher chemical activity than O₂. Although ROS pose potential risks to all organisms via inducing oxidative stress, indispensable role of ROS in individual development cannot be ignored. Among them, the role of ROS in the model plant Arabidopsis thaliana is deeply studied. Mounting evidence suggests that ROS are essential for root and root hair development. In the present review, we provide an updated perspective on the latest research progress pertaining to the role of ROS in the precise regulation of root stem cell maintenance and differentiation, redox regulation of the cell cycle, and root hair initiation during root growth. Among the different types of ROS, O₂ ^•- and H₂O₂ have been extensively investigated, and they exhibit different gradient distributions in the roots. The concentration of O₂ ^•- decreases along a gradient from the meristem to the transition zone and the concentration of H₂O₂ decreases along a gradient from the differentiation zone to the elongation zone. These gradients are regulated by peroxidases, which are modulated by the UPBEAT1 (UPB1) transcription factor. In addition, multiple transcriptional factors, such as APP1, ABO8, PHB3, and RITF1, which are involved in the brassinolide signaling pathway, converge as a ROS signal to regulate root stem cell maintenance. Furthermore, superoxide anions (O₂ ^•-) are generated from the oxidation in mitochondria, ROS produced during plasmid metabolism, H₂O₂ produced in apoplasts, and catalysis of respiratory burst oxidase homolog (RBOH) in the cell membrane. Furthermore, ROS can act as a signal to regulate redox status, which regulates the expression of the cell-cycle components CYC2;3, CYCB1;1, and retinoblastoma-related protein, thereby controlling the cell-cycle progression. In the root maturation zone, the epidermal cells located in the H cell position emerge to form hair cells, and plant hormones, such as auxin and ethylene regulate root hair formation via ROS. Furthermore, ROS accumulation can influence hormone signal transduction and vice versa. Data about the association between nutrient stress and ROS signals in root hair development are scarce. However, the fact that ROBHC/RHD2 or RHD6 is specifically expressed in root hair cells and induced by nutrients, may explain the relationship. Future studies should focus on the regulatory mechanisms underlying root hair development via the interactions of ROS with hormone signals and nutrient components.

Integrative analysis of hexaploid wheat roots identifies signature components during iron starvation

Iron (Fe) is an essential micronutrient for all organisms. In crop plants, Fe deficiency can decrease crop yield significantly; however, our current understanding of how major crops respond to Fe deficiency remains limited. Herein, the effect of Fe deprivation at both the transcriptomic and metabolic level in hexaploid wheat was investigated. Genome-wide gene expression reprogramming was observed in wheat roots subjected to Fe starvation, with a total of 5854 genes differentially expressed. Homoeologue and subgenome-specific analysis unveiled the induction-biased contribution from the A and B genomes. In general, the predominance of genes coding for nicotianamine synthase, yellow stripe-like transporters, metal transporters, ABC transporters, and zinc-induced facilitator-like protein was noted. Expression of genes related to the Strategy II mode of Fe uptake was also predominant. Our transcriptomic data were in agreement with the GC-MS analysis that showed the enhanced accumulation of various metabolites such as fumarate, malonate, succinate, and xylofuranose, which could be contributing to Fe mobilization. Interestingly, Fe starvation leads to a significant temporal increase of glutathione S-transferase at both the transcriptional level and enzymatic activity level, which indicates the involvement of glutathione in response to Fe stress in wheat roots. Taken together, our result provides new insight into the wheat response to Fe starvation at the molecular level and lays the foundation to design new strategies for the improvement of Fe nutrition in crops.

Contribution of Root Hair Development to Sulfate Uptake in Arabidopsis

Root hairs often contribute to nutrient uptake from environments, but the contribution varies among nutrients. In Arabidopsis, two high-affinity sulfate transporters, SULTR1;1 and SULTR1;2, are responsible for sulfate uptake by roots. Their increased expression under sulfur deficiency (-S) stimulates sulfate uptake. Inspired by the higher and lower expression, respectively, of SULTR1;1 in mutants with more (werwolf [wer]) and fewer (caprice [cpc]) root hairs, we examined the contribution of root hairs to sulfate uptake. Sulfate uptake rates were similar among plant lines under both sulfur sufficiency (+S) and -S. Under -S, the expression of SULTR1;1 and SULTR1;2 was negatively correlated with the number of root hairs. These results suggest that both -S-induced SULTR expression and sulfate uptake rates were independent of the number of root hairs. In addition, we observed (1) a negative correlation between primary root lengths and number of root hairs and (2) a greater number of root hairs under -S than under +S. These observations suggested that under both +S and -S, sulfate uptake was influenced by the root biomass rather than the number of root hairs.

The basic helix-loop-helix transcription factor, bHLH11 functions in the iron-uptake system in Arabidopsis thaliana

Iron (Fe) is a micronutrient that is essential for plant development and growth. Basic helix-loop-helix (bHLH) transcription factors are a superfamily of transcription factors that are important regulatory components in transcriptional networks in plants. bHLH transcription factors have been divided into subclasses based on their amino acid sequences and domain structures. Among the members of clade IVb (PYE, bHLH121, and bHLH11), the functions of bHLH11 remain unclear. In the present study, we characterized bHLH11 as a negative regulator of Fe homeostasis. bHLH11 expression levels were high in the roots and up-regulated after plants were transferred to Fe sufficient conditions. Although T-DNA knockout mutants of bHLH11 were lethal, dominant negative (DN-) and overexpression (OX-) of bHLH11 plants exhibited sensitivity to Fe deficiency. Furthermore, the expression of FIT, a master regulator of Fe deficiency responses, was suppressed in the transgenic plants. These results suggest that the transcriptional repressor bHLH11 functions as a negative regulator of FIT-dependent Fe uptake and modulates Fe levels in Arabidopsis plants. Salicylic acid (SA) modulates the expression of genes involved in Fe-deficient responses. We found that SA levels were elevated in DN- and OX-bHLH11 plants. The T-DNA insertion mutant sid2-1, which was defective for the production of SA, did not exhibit sensitivity to Fe deficiency; however, the crossed plants of OX-bHLH11 and sid2-1 relieved sensitivity to the Fe deficiency observed in OX-bHLH11 plants. These results suggest that the accumulation of SA is closely related to iron homeostasis.

Buffered delivery of phosphate to Arabidopsis alters responses to low phosphate

Arabidopsis has been reported to respond to phosphate (Pi) stress by arresting primary root growth and increasing lateral root branching. We developed a system to buffer Pi availability to Arabidopsis in gel media systems by charging activated aluminum oxide particles with low and sufficient concentrations of Pi, based on previous work in horticultural and sand culture systems. This system more closely mimics soil chemistry and results in different growth and transcriptional responses to Pi stress compared with plants grown in standard gel media. Low Pi availability in buffered medium results in reduced root branching and preferential investment of resources in axial root growth. Root hair length and density, known responses to Pi stress, increase in low-buffered Pi medium. Plants grown under buffered Pi conditions have different gene expression profiles of canonical Pi stress response genes as compared with their unbuffered counterparts. The system also eliminates known complications with iron (Fe) nutrition. The growth responses of Arabidopsis supplied with buffered Pi indicate that the widely accepted low-Pi phenotype is an artifact of the standard gel-based growth system. Buffering Pi availability through the method presented here will improve the utility and accuracy of gel studies by more closely approximating soil conditions.

Airborne signals from Trichoderma fungi stimulate iron uptake responses in roots resulting in priming of jasmonic acid-dependent defences in shoots of Arabidopsis thaliana and Solanum lycopersicum

Root colonization by Trichoderma fungi can trigger induced systemic resistance (ISR). In Arabidopsis, Trichoderma-ISR relies on the transcription factor MYB72, which plays a dual role in the onset of ISR and the activation of Fe uptake responses. Volatile compounds (VCs) from rhizobacteria are important elicitors of MYB72 in Arabidopsis roots. Here, we investigated the mode of action of VCs from Trichoderma fungi in the onset of ISR and Fe uptake responses. VCs from Trichoderma asperellum and Trichoderma harzianum were applied in an in vitro split-plate system with Arabidopsis or tomato seedlings. Locally, Trichoderma-VCs triggered MYB72 expression and molecular, physiological and morphological Fe uptake mechanisms in Arabidopsis roots. In leaves, Trichoderma-VCs primed jasmonic acid-dependent defences, leading to an enhanced resistance against Botrytis cinerea. By using Arabidopsis micrografts of VCs-exposed rootstocks and non-exposed scions, we demonstrated that perception of Trichoderma-VCs by the roots leads to a systemic signal that primes shoots for enhanced defences. Trichoderma-VCs also elicited Fe deficiency responses and shoot immunity in tomato, suggesting that this phenomenon is expressed in different plant species. Our results indicate that Trichoderma-VCs trigger locally a readjustment of Fe homeostasis in roots, which links to systemic elicitation of ISR by priming of jasmonic acid-dependent defences.

Arabidopsis Glutaredoxin S17 Contributes to Vegetative Growth, Mineral Accumulation, and Redox Balance during Iron Deficiency

Iron (Fe) is an essential mineral nutrient and a metal cofactor required for many proteins and enzymes involved in the processes of DNA synthesis, respiration, and photosynthesis. Iron limitation can have detrimental effects on plant growth and development. Such effects are mediated, at least in part, through the generation of reactive oxygen species (ROS). Thus, plants have evolved a complex regulatory network to respond to conditions of iron limitations. However, the mechanisms that couple iron deficiency and oxidative stress responses are not fully understood. Here, we report the discovery that an Arabidopsis thaliana monothiol glutaredoxin S17 (AtGRXS17) plays a critical role in the plants ability to respond to iron deficiency stress and maintain redox homeostasis. In a yeast expression assay, AtGRXS17 was able to suppress the iron accumulation in yeast ScGrx3/ScGrx4 mutant cells. Genetic analysis indicated that plants with reduced AtGRXS17 expression were hypersensitive to iron deficiency and showed increased iron concentrations in mature seeds. Disruption of AtGRXS17 caused plant sensitivity to exogenous oxidants and increased ROS production under iron deficiency. Addition of reduced glutathione rescued the growth and alleviates the sensitivity of atgrxs17 mutants to iron deficiency. These findings suggest AtGRXS17 helps integrate redox homeostasis and iron deficiency responses.

H+ -pyrophosphatase IbVP1 promotes efficient iron use in sweet potato [Ipomoea batatas (L.) Lam.]

Iron (Fe) deficiency is one of the most common micronutrient deficiencies limiting crop production globally, especially in arid regions because of decreased availability of iron in alkaline soils. Sweet potato [Ipomoea batatas (L.) Lam.] grows well in arid regions and is tolerant to Fe deficiency. Here, we report that the transcription of type I H+ -pyrophosphatase (H+ -PPase) gene IbVP1 in sweet potato plants was strongly induced by Fe deficiency and auxin in hydroponics, improving Fe acquisition via increased rhizosphere acidification and auxin regulation. When overexpressed, transgenic plants show higher pyrophosphate hydrolysis and plasma membrane H+ -ATPase activity compared with the wild type, leading to increased rhizosphere acidification. The IbVP1-overexpressing plants showed better growth, including enlarged root systems, under Fe-sufficient or Fe-deficient conditions. Increased ferric precipitation and ferric chelate reductase activity in the roots of transgenic lines indicate improved iron uptake, which is also confirmed by increased Fe content and up-regulation of Fe uptake genes, e.g. FRO2, IRT1 and FIT. Carbohydrate metabolism is significantly affected in the transgenic lines, showing increased sugar and starch content associated with the increased expression of AGPase and SUT1 genes and the decrease in β-amylase gene expression. Improved antioxidant capacities were also detected in the transgenic plants, which showed reduced H2 O2 accumulation associated with up-regulated ROS-scavenging activity. Therefore, H+ -PPase plays a key role in the response to Fe deficiency by sweet potato and effectively improves the Fe acquisition by overexpressing IbVP1 in crops cultivated in micronutrient-deficient soils.

Natural allelic variation of FRO2 modulates Arabidopsis root growth under iron deficiency

Low availability of Fe significantly limits crop yields in many parts of the world. However, it is largely unknown which genes and alleles adjust plant growth in Fe limited environments. Using natural variation of a geographically restricted panel of Arabidopsis thaliana accessions, we identify allelic variation at the FRO2 locus associated with root length under iron deficiency. We show that non-coding sequence variation at the FRO2 locus leads to variation of FRO2 transcript levels, as well as ferric chelate reductase activity, and is causal for a portion of the observed root length variation. These FRO2 allele dependent differences are coupled with altered seedling phenotypes grown on iron-limited soil. Overall, we show that these natural genetic variants of FRO2 tune its expression. These variants might be useful for improvement of agronomically relevant species under specific environmental conditions, such as in podzols or calcareous soils.

Iron is an essential micronutrient for plants and a lack of iron availability limits crop yield in many parts of the world. Here the authors show that natural variation in root growth of Arabidopsis plants under iron deficiency can be caused by allelic variation at the FRO2 locus.

The Understanding of the Plant Iron Deficiency Responses in Strategy I Plants and the Role of Ethylene in This Process by Omic Approaches

Iron (Fe) is an essential plant micronutrient but is toxic in excess. Fe deficiency chlorosis is a major constraint for plant growth and causes severe losses of crop yields and quality. Under Fe deficiency conditions, plants have developed sophisticated mechanisms to keep cellular Fe homeostasis via various physiological, morphological, metabolic, and gene expression changes to facilitate the availability of Fe. Ethylene has been found to be involved in the Fe deficiency responses of plants through pharmacological studies or by the use of ethylene mutants. However, how ethylene is involved in the regulations of Fe starvation responses remains not fully understood. Over the past decade, omics approaches, mainly focusing on the RNA and protein levels, have been used extensively to investigate global gene expression changes under Fe-limiting conditions, and thousands of genes have been found to be regulated by Fe status. Similarly, proteome profiles have uncovered several hallmark processes that help plants adapt to Fe shortage. To find out how ethylene participates in the Fe deficiency response and explore putatively novel regulators for further investigation, this review emphasizes the integration of those genes and proteins, derived from omics approaches, regulated both by Fe deficiency, and ethylene into a systemic network by gene co-expression analysis.

Arabidopsis Glutaredoxin S17 Contributes to Vegetative Growth, Mineral Accumulation, and Redox Balance during Iron Deficiency

Iron (Fe) is an essential mineral nutrient and a metal cofactor required for many proteins and enzymes involved in the processes of DNA synthesis, respiration, and photosynthesis. Iron limitation can have detrimental effects on plant growth and development. Such effects are mediated, at least in part, through the generation of reactive oxygen species (ROS). Thus, plants have evolved a complex regulatory network to respond to conditions of iron limitations. However, the mechanisms that couple iron deficiency and oxidative stress responses are not fully understood. Here, we report the discovery that an Arabidopsis thaliana monothiol glutaredoxin S17 (AtGRXS17) plays a critical role in the plants ability to respond to iron deficiency stress and maintain redox homeostasis. In a yeast expression assay, AtGRXS17 was able to suppress the iron accumulation in yeast ScGrx3/ScGrx4 mutant cells. Genetic analysis indicated that plants with reduced AtGRXS17 expression were hypersensitive to iron deficiency and showed increased iron concentrations in mature seeds. Disruption of AtGRXS17 caused plant sensitivity to exogenous oxidants and increased ROS production under iron deficiency. Addition of reduced glutathione rescued the growth and alleviates the sensitivity of atgrxs17 mutants to iron deficiency. These findings suggest AtGRXS17 helps integrate redox homeostasis and iron deficiency responses.

Evolutionary analysis of iron (Fe) acquisition system in Marchantia polymorpha

To acquire appropriate iron (Fe), vascular plants have developed two unique strategies, the reduction-based strategy I of nongraminaceous plants for Fe(2+) and the chelation-based strategy II of graminaceous plants for Fe(3+) . However, the mechanism of Fe uptake in bryophytes, the earliest diverging branch of land plants and dominant in gametophyte generation is less clear. Fe isotope fractionation analysis demonstrated that the liverwort Marchantia polymorpha uses reduction-based Fe acquisition. Enhanced activities of ferric chelate reductase and proton ATPase were detected under Fe-deficient conditions. However, M. polymorpha did not show mugineic acid family phytosiderophores, the key components of strategy II, or the precursor nicotianamine. Five ZIP (ZRT/IRT-like protein) homologs were identified and speculated to be involved in Fe uptake in M. polymorpha. MpZIP3 knockdown conferred reduced growth under Fe-deficient conditions, and MpZIP3 overexpression increased Fe content under excess Fe. Thus, a nonvascular liverwort, M. polymorpha, uses strategy I for Fe acquisition. This system may have been acquired in the common ancestor of land plants and coopted from the gametophyte to sporophyte generation in the evolution of land plants.

Vigorous Root Growth Is a Better Indicator of Early Nutrient Uptake than Root Hair Traits in Spring Wheat Grown under Low Fertility

A number of root and root hair traits have been proposed as important for nutrient acquisition. However, there is still a need for knowledge on which traits are most important in determining macro- and micronutrient uptake at low soil fertility. This study investigated the variations in root growth vigor and root hair length (RHL) and density (RHD) among spring wheat genotypes and their relationship to nutrient concentrations and uptake during early growth. Six spring wheat genotypes were grown in a soil with low nutrient availability. The root and root hair traits as well as the concentration and content of macro- and micronutrients were identified. A significant genetic variability in root and root hair traits as well as nutrient uptake was found. Fast and early root proliferation and long and dense root hairs enhanced uptake of macro- and micronutrients under low soil nutrient availability. Vigorous root growth, however, was a better indicator of early nutrient acquisition than RHL and RHD. Vigorous root growth and long and dense root hairs ensured efficient acquisition of macro- and micronutrients during early growth and a high root length to shoot dry matter ratio favored high macronutrient concentrations in the shoots, which is assumed to be important for later plant development.

The Response of the Root Apex in Plant Adaptation to Iron Heterogeneity in Soil

Iron (Fe) is an essential micronutrient for plant growth and development, and is frequently limiting. By contrast, over-accumulation of Fe in plant tissues leads to toxicity. In soils, the distribution of Fe is highly heterogeneous. To cope with this heterogeneity, plant roots engage an array of adaptive responses to adjust their morphology and physiology. In this article, we review root morphological and physiological changes in response to low- and high-Fe conditions and highlight differences between these responses. We especially focus on the role of the root apex in dealing with the stresses resulting from Fe shortage and excess.

Increased Sucrose Accumulation Regulates Iron-Deficiency Responses by Promoting Auxin Signaling in Arabidopsis Plants

Previous studies have identified that auxins acts upstream of nitric oxide in regulating iron deficiency responses in roots, but the upstream signaling molecule of auxins remains unknown. In this study, we showed that Fe deficiency increased sucrose (Suc) level in roots of Arabidopsis (Arabidopsis thaliana). Exogenous application of Suc further stimulated Fe deficiency-induced ferric-chelate-reductase (FCR) activity and expression of Fe acquisition-related genes FRO2, IRT1, and FIT in roots. The opposite patterns were observed in the dark treatment. In addition, FCR activity and expression of Fe acquisition-related genes were higher in the Suc high-accumulating transgenic plant 35S::SUC2 but were lower in the Suc low-accumulating mutant suc2-5 compared with wild-type plants under Fe-deficient conditions. Consequently, Fe deficiency tolerance was enhanced in 35S::SUC2 but was compromised in suc2-5. Exogenous Suc also increased root β-glucuronidase (GUS) activity in auxin-inducible reporter DR5-GUS transgenic plants under Fe deficiency. However, exogenous Suc failed to increase FCR activity and expression of Fe acquisition-related genes in the auxin transport-impaired mutants aux1-7 and pin1-1 as well as in the wild-type plants treated with an auxin transport inhibitor under Fe deficiency. In summary, we found that increased Suc accumulation is required for regulating Fe deficiency responses in plants, with auxins acting downstream in transmitting the Fe deficiency signal.

Adaptation of Root Function by Nutrient-Induced Plasticity of Endodermal Differentiation

Plant roots forage the soil for minerals whose concentrations can be orders of magnitude away from those required for plant cell function. Selective uptake in multicellular organisms critically requires epithelia with extracellular diffusion barriers. In plants, such a barrier is provided by the endodermis and its Casparian strips--cell wall impregnations analogous to animal tight and adherens junctions. Interestingly, the endodermis undergoes secondary differentiation, becoming coated with hydrophobic suberin, presumably switching from an actively absorbing to a protective epithelium. Here, we show that suberization responds to a wide range of nutrient stresses, mediated by the stress hormones abscisic acid and ethylene. We reveal a striking ability of the root to not only regulate synthesis of suberin, but also selectively degrade it in response to ethylene. Finally, we demonstrate that changes in suberization constitute physiologically relevant, adaptive responses, pointing to a pivotal role of the endodermal membrane in nutrient homeostasis.

Nanotechnology promotes the R&D of new-generation micronutrient foliar fertilizers

New generation foliar fertilizers are expected to be sheet-like nanocrystals and provide a sustainable supply of metal ions at a suitable concentration.

Ethylene Participates in the Regulation of Fe Deficiency Responses in Strategy I Plants and in Rice

Iron (Fe) is very abundant in most soils but its availability for plants is low, especially in calcareous soils. Plants have been divided into Strategy I and Strategy II species to acquire Fe from soils. Strategy I species apply a reduction-based uptake system which includes all higher plants except the Poaceae. Strategy II species apply a chelation-based uptake system which includes the Poaceae. To cope with Fe deficiency both type of species activate several Fe deficiency responses, mainly in their roots. These responses need to be tightly regulated to avoid Fe toxicity and to conserve energy. Their regulation is not totally understood but some hormones and signaling substances have been implicated. Several years ago it was suggested that ethylene could participate in the regulation of Fe deficiency responses in Strategy I species. In Strategy II species, the role of hormones and signaling substances has been less studied. However, in rice, traditionally considered a Strategy II species but that possesses some characteristics of Strategy I species, it has been recently shown that ethylene can also play a role in the regulation of some of its Fe deficiency responses. Here, we will review and discuss the data supporting a role for ethylene in the regulation of Fe deficiency responses in both Strategy I species and rice. In addition, we will review the data about ethylene and Fe responses related to Strategy II species. We will also discuss the results supporting the action of ethylene through different transduction pathways and its interaction with other signals, such as certain Fe-related repressive signals occurring in the phloem sap. Finally, the possible implication of ethylene in the interactions among Fe deficiency responses and the responses to other nutrient deficiencies in the plant will be addressed.

Deciphering Mineral Homeostasis in Barley Seed Transfer Cells at Transcriptional Level

In addition to the micronutrient inadequacy of staple crops for optimal human nutrition, a global downtrend in crop-quality has emerged from intensive breeding for yield. This trend will be aggravated by elevated levels of the greenhouse gas carbon dioxide. Therefore, crop biofortification is inevitable to ensure a sustainable supply of minerals to the large part of human population who is dietary dependent on staple crops. This requires a thorough understanding of plant-mineral interactions due to the complexity of mineral homeostasis. Employing RNA sequencing, we here communicate transfer cell specific effects of excess iron and zinc during grain filling in our model crop plant barley. Responding to alterations in mineral contents, we found a long range of different genes and transcripts. Among them, it is worth to highlight the auxin and ethylene signaling factors Arfs, Abcbs, Cand1, Hps4, Hac1, Ecr1, and Ctr1, diurnal fluctuation components Sdg2, Imb1, Lip1, and PhyC, retroelements, sulfur homeostasis components Amp1, Hmt3, Eil3, and Vip1, mineral trafficking components Med16, Cnnm4, Aha2, Clpc1, and Pcbps, and vacuole organization factors Ymr155W, RabG3F, Vps4, and Cbl3. Our analysis introduces new interactors and signifies a broad spectrum of regulatory levels from chromatin remodeling to intracellular protein sorting mechanisms active in the plant mineral homeostasis. The results highlight the importance of storage proteins in metal ion toxicity-resistance and chelation. Interestingly, the protein sorting and recycling factors Exoc7, Cdc1, Sec23A, and Rab11A contributed to the response as well as the polar distributors of metal-transporters ensuring the directional flow of minerals. Alternative isoform switching was found important for plant adaptation and occurred among transcripts coding for identical proteins as well as transcripts coding for protein isoforms. We also identified differences in the alternative-isoform preference between the treatments, indicating metal-affinity shifts among isoforms of metal transporters. Most important, we found the zinc treatment to impair both photosynthesis and respiration. A wide range of transcriptional changes including stress-related genes and negative feedback loops emphasize the importance to withhold mineral contents below certain cellular levels which otherwise might lead to agronomical impeding side-effects. By illustrating new mechanisms, genes, and transcripts, this report provides a solid platform towards understanding the complex network of plant mineral homeostasis.

Rhizobacterial volatiles and photosynthesis-related signals coordinate MYB72 expression in Arabidopsis roots during onset of induced systemic resistance and iron-deficiency responses

In Arabidopsis roots, the transcription factor MYB72 plays a dual role in the onset of rhizobacteria-induced systemic resistance (ISR) and plant survival under conditions of limited iron availability. Previously, it was shown that MYB72 coordinates the expression of a gene module that promotes synthesis and excretion of iron-mobilizing phenolic compounds in the rhizosphere, a process that is involved in both iron acquisition and ISR signaling. Here, we show that volatile organic compounds (VOCs) from ISR-inducing Pseudomonas bacteria are important elicitors of MYB72. In response to VOC treatment, MYB72 is co-expressed with the iron uptake-related genes FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER 1 (IRT1) in a manner that is dependent on FER-LIKE IRON DEFICIENCY TRANSCRIPTION FACTOR (FIT), indicating that MYB72 is an intrinsic part of the plant's iron-acquisition response that is typically activated upon iron starvation. However, VOC-induced MYB72 expression is activated independently of iron availability in the root vicinity. Moreover, rhizobacterial VOC-mediated induction of MYB72 requires photosynthesis-related signals, while iron deficiency in the rhizosphere activates MYB72 in the absence of shoot-derived signals. Together, these results show that the ISR- and iron acquisition-related transcription factor MYB72 in Arabidopsis roots is activated by rhizobacterial volatiles and photosynthesis-related signals, and enhances the iron-acquisition capacity of roots independently of the iron availability in the rhizosphere. This work highlights the role of MYB72 in plant processes by which root microbiota simultaneously stimulate systemic immunity and activate the iron-uptake machinery in their host plants.

Ethylene and the Regulation of Physiological and Morphological Responses to Nutrient Deficiencies

To cope with nutrient deficiencies, plants develop both morphological and physiological responses. The regulation of these responses is not totally understood, but some hormones and signaling substances have been implicated. It was suggested several years ago that ethylene participates in the regulation of responses to iron and phosphorous deficiency. More recently, its role has been extended to other deficiencies, such as potassium, sulfur, and others. The role of ethylene in so many deficiencies suggests that, to confer specificity to the different responses, it should act through different transduction pathways and/or in conjunction with other signals. In this update, the data supporting a role for ethylene in the regulation of responses to different nutrient deficiencies will be reviewed. In addition, the results suggesting the action of ethylene through different transduction pathways and its interaction with other hormones and signaling substances will be discussed.

Iron- and ferritin-dependent reactive oxygen species distribution: impact on Arabidopsis root system architecture

Iron (Fe) homeostasis is integrated with the production of reactive oxygen species (ROS), and distribution at the root tip participates in the control of root growth. Excess Fe increases ferritin abundance, enabling the storage of Fe, which contributes to protection of plants against Fe-induced oxidative stress. AtFer1 and AtFer3 are the two ferritin genes expressed in the meristematic zone, pericycle and endodermis of the Arabidopsis thaliana root, and it is in these regions that we observe Fe stained dots. This staining disappears in the triple fer1-3-4 ferritin mutant. Fe excess decreases primary root length in the same way in wild-type and in fer1-3-4 mutant. In contrast, the Fe-mediated decrease of lateral root (LR) length and density is enhanced in fer1-3-4 plants due to a defect in LR emergence. We observe that this interaction between excess Fe, ferritin, and root system architecture (RSA) is in part mediated by the H2O2/O2·- balance between the root cell proliferation and differentiation zones regulated by the UPB1 transcription factor. Meristem size is also decreased in response to Fe excess in ferritin mutant plants, implicating cell cycle arrest mediated by the ROS-activated SMR5/SMR7 cyclin-dependent kinase inhibitors pathway in the interaction between Fe and RSA.

OsARF16, a transcription factor regulating auxin redistribution, is required for iron deficiency response in rice (Oryza sativa L.)

Plant response to iron deficiency is the most important feature for survival in Fe-limited soils. Several phytohormones, including auxin, are involved in iron uptake and homeostasis. However, the mechanisms behind how auxin participates in the iron deficiency response in rice are largely unknown. We found that OsARF16 was involved in the iron deficiency response and the induction of iron deficiency response genes. Most Fe-deficient symptoms could be partially restored in the osarf16 mutant, including dwarfism, photosynthesis decline, a reduction in iron content and root system architecture (RSA) regulation. OsARF16 expression was induced in the roots and shoots by Fe deprivation. Restoration of the phenotype could also be mimicked by 1-NOA, an auxin influx inhibitor. Furthermore, the qRT-PCR data indicated that the induction of Fe-deficiency response genes by iron deficiency was more compromised in the osarf16 mutant than in Nipponbare. In conclusion, osarf16, an auxin insensitive mutant, was involved in iron deficiency response in rice. Our results reveal a new biological function for OsARF16 and provide important information on how ARF-medicated auxin signaling affects iron signaling and the iron deficiency response. This work may help us to improve production or increased Fe nutrition of rice to iron deficiency by regulating auxin signaling.

Magnesium availability regulates the development of root hairs in Arabidopsis thaliana (L.) Heynh

Root hairs are reported to be plastic in response to nutrient supply, but relatively little is known about their development in response to magnesium (Mg) availability. Here, we showed that development of root hairs of Arabidopsis decreased progressively with increasing Mg supply, which was related to the initiation of new trichoblast files and likelihood of trichoblasts to form hairs. Tip-focused reactive oxygen species (ROS) and cytosolic Ca(2+) concentrations [(Ca(2+) )c] during elongation of root hairs were enhanced under low Mg but decreased under high Mg. Under low Mg, application of diphenylene iodonium (DPI) or BAPTA [1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid] blocked the enhanced development of root hairs and the opposite was true when the plants under high Mg were treated with phenazine methosulphate (PMS), methyl viologen (MV) or CaCl2 . Furthermore, Mg availability did not alter root hair growth in rhd2-1 mutant that contains lower levels of ROS and cytosolic [Ca(2+) ]c. Transcriptome data and qPCR results revealed a greater fraction of morphogenetic H-genes, and cell wall organization genes were up-regulated by low Mg but down-regulated by high Mg. Our data suggest a profound effect of Mg supply on the development of root hairs in Arabidopsis, through the characterized Ca(2+) and ROS signals that modulate the elongation of root hairs and the expression of root-hair morphogenetic genes.

Natural variation of root traits: from development to nutrient uptake

The root system has a crucial role for plant growth and productivity. Due to the challenges of heterogeneous soil environments, diverse environmental signals are integrated into root developmental decisions. While root growth and growth responses are genetically determined, there is substantial natural variation for these traits. Studying the genetic basis of the natural variation of root growth traits can not only shed light on their evolution and ecological relevance but also can be used to map the genes and their alleles responsible for the regulation of these traits. Analysis of root phenotypes has revealed growth strategies and root growth responses to a variety of environmental stimuli, as well as the extent of natural variation of a variety of root traits including ion content, cellular properties, and root system architectures. Linkage and association mapping approaches have uncovered causal genes underlying the variation of these traits.

Root hairs

Roots hairs are cylindrical extensions of root epidermal cells that are important for acquisition of nutrients, microbe interactions, and plant anchorage. The molecular mechanisms involved in the specification, differentiation, and physiology of root hairs in Arabidopsis are reviewed here. Root hair specification in Arabidopsis is determined by position-dependent signaling and molecular feedback loops causing differential accumulation of a WD-bHLH-Myb transcriptional complex. The initiation of root hairs is dependent on the RHD6 bHLH gene family and auxin to define the site of outgrowth. Root hair elongation relies on polarized cell expansion at the growing tip, which involves multiple integrated processes including cell secretion, endomembrane trafficking, cytoskeletal organization, and cell wall modifications. The study of root hair biology in Arabidopsis has provided a model cell type for insights into many aspects of plant development and cell biology.

Characteristics of a root hair-less line of Arabidopsis thaliana under physiological stresses

The plasma membrane-associated Ca(2+)-binding protein-2 of Arabidopsis thaliana is involved in the growth of root hair tips. Several transgenic lines that overexpress the 23 residue N-terminal domain of this protein under the control of the root hair-specific EXPANSIN A7 promoter lack root hairs completely. The role of root hairs under normal and stress conditions was examined in one of these root hair-less lines (NR23). Compared with the wild type, NR23 showed a 47% reduction in water absorption, decreased drought tolerance, and a lower ability to adapt to heat. Growth of NR23 was suppressed in media deficient in phosphorus, iron, calcium, zinc, copper, or potassium. Also, the content of an individual mineral in NR23 grown in normal medium, or in medium lacking a specific mineral, was relatively low. In wild-type plants, the primary and lateral roots produce numerous root hairs that become elongated under phosphate-deficient conditions; NR23 did not produce root hairs. Although several isoforms of the plasma membrane phosphate transporters including PHT1;1-PHT1;6 were markedly induced after growth in phosphate-deficient medium, the levels induced in NR23 were less than half those observed in the wild type. In phosphate-deficient medium, the amounts of acid phosphatase, malate, and citrate secreted from NR23 roots were 38, 9, and 16% of the levels secreted from wild-type roots. The present results suggest that root hairs play significant roles in the absorption of water and several minerals, secretion of acid phosphatase(s) and organic acids, and in penetration of the primary roots into gels.