Moving up, down, and everywhere: signaling of micronutrients in plants

Cross-Talk between Iron Deficiency Response and Defense Establishment in Plants

Plants are at risk of attack by various pathogenic organisms. During pathogenesis, microorganisms produce molecules with conserved structures that are recognized by plants that then initiate a defense response. Plants also experience iron deficiency. To address problems caused by iron deficiency, plants use two strategies focused on iron absorption from the rhizosphere. Strategy I is based on rhizosphere acidification and iron reduction, whereas Strategy II is based on iron chelation. Pathogenic defense and iron uptake are not isolated phenomena: the antimicrobial phenols are produced by the plant during defense, chelate and solubilize iron; therefore, the production and secretion of these molecules also increase in response to iron deficiency. In contrast, phytohormone jasmonic acid and salicylic acid that induce pathogen-resistant genes also modulate the expression of genes related to iron uptake. Iron deficiency also induces the expression of defense-related genes. Therefore, in the present review, we address the cross-talk that exists between the defense mechanisms of both Systemic Resistance and Systemic Acquired Resistance pathways and the response to iron deficiency in plants, with particular emphasis on the regulation genetic expression.

Truncated hemoglobin 2 modulates phosphorus deficiency response by controlling of gene expression in nitric oxide-dependent pathway in Chlamydomonas reinhardtii

Truncated hemoglobin 2 is involved in fine-tuning of PSR1-regulated gene expression during phosphorus deprivation. Truncated hemoglobins form a large family found in all domains of life. However, a majority of physiological functions of these proteins remain to be elucidated. In the model alga Chlamydomonas reinhardtii, macro-nutritional deprivation is known to elevate truncated hemoglobin 2 (THB2). This study investigated the role of THB2 in the regulation of a subset of phosphorus (P) limitation-responsive genes in cells suffering from P-deficiency. Underexpression of THB2 in amiTHB2 strains resulted in downregulation of a suite of P deprivation-induced genes encoding proteins with different subcellular location and functions (e.g., PHOX, LHCSR3.1, LHCSR3.2, PTB2, and PTB5). Moreover, our results provided primary evidence that the soluble guanylate cyclase 12 gene (CYG12) is a component of the P deprivation regulation. Furthermore, the transcription of PSR1 gene for the most critical regulator in the acclimation process under P restriction was repressed by nitric oxide (NO). Collectively, the results indicated a tight regulatory link between the THB2-controlled NO levels and PSR1-dependent induction of several P deprivation responsive genes with various roles in cells during P-limitation.

Ethylene regulates sulfur acquisition by regulating the expression of sulfate transporter genes in oilseed rape

To manage nutrient deficiencies, plants develop both morphological and physiological responses. The studies on the regulation of these responses are limited; however, certain hormones and signaling components have been largely implicated. Several studies depicted ethylene as a regulator of the response of some nutrient deficiencies like iron, phosphorous and potassium. The present study focused on the response of sulfur in the presence and absence of ethylene. The experiments were performed in hydroponic nutrient media, using oilseed rape grown with or without sulfur deficiency and ethylene treatments for 10 days. The ACC oxidase and ACC synthase were observed significantly reduced in sulfur-deficient plants treated with ethylene compared to control. The biomass and photosynthetic parameters, including the expression of multicomplex thylakoidal proteins showed a significant increase in sulfur deficient plants supplemented with ethylene. The enzymes related to sulfur regulation such as sulfate adenyltransferase, glutamine synthetase and O-acetylserine (thiol)lyase also showed similar results as shown by the morphological data. The relative expression of the sulfur transporter genes BnSultr1, 1, BnSultr1, 2, BnSultr4,1, BnSultr 4,2, ATP sulfurylase and OASTL increased in sulfur-deficient plants, whereas their expression decreased when ethylene was given to the plants. Fe and S nutritional correlations are already known; therefore, Fe-transporters like IRT1 and FRO1 were also evaluated, and similar results as for the sulfur transporter genes were observed. The overall results indicated that ethylene regulates sulfur acquisition by regulating the expression of sulfur transporter genes in oilseed rape (Brassica napus).

Interaction Between Macro- and Micro-Nutrients in Plants

Nitrogen (N), phosphorus (P), sulfur (S), zinc (Zn), and iron (Fe) are some of the vital nutrients required for optimum growth, development, and productivity of plants. The deficiency of any of these nutrients may lead to defects in plant growth and decreased productivity. Plant responses to the deficiency of N, P, S, Fe, or Zn have been studied mainly as a separate event, and only a few reports discuss the molecular basis of biological interaction among the nutrients. Macro-nutrients like N, P, and/or S not only show the interacting pathways for each other but also affect micro-nutrient pathways. Limited reports are available on the investigation of two-by-two or multi-level nutrient interactions in plants. Such studies on the nutrient interaction pathways suggest that an MYB-like transcription factor, phosphate starvation response 1 (PHR1), acts as a master regulator of N, P, S, Fe, and Zn homeostasis. Similarly, light-responsive transcription factors were identified to be involved in modulating nutrient responses in Arabidopsis. This review focuses on the recent advances in our understanding of how plants coordinate the acquisition, transport, signaling, and interacting pathways for N, P, S, Fe, and Zn nutrition at the molecular level. Identification of the important candidate genes for interactions between N, P, S, Fe, and/or Zn metabolic pathways might be useful for the breeders to improve nutrient use efficiency and yield/quality of crop plants. Integrated studies on pathways interactions/cross-talks between macro- and micro-nutrients in the agronomically important crop plants would be essential for sustainable agriculture around the globe, particularly under the changing climatic conditions.

Glutamate synthase 1 is involved in iron-deficiency response and long-distance transportation in Arabidopsis

Iron is an essential microelement for plant growth. After uptake from the soil, iron is chelated by ligands and translocated from roots to shoots for subsequent utilization. However, the number of ligands involved in iron chelation is unclear. In this study, we identified and demonstrated that GLU1, which encodes a ferredoxin-dependent glutamate synthase, was involved in iron homeostasis. First, the expression of GLU1 was strongly induced by iron deficiency condition. Second, lesion of GLU1 results in reduced transcription of many iron-deficiency-responsive genes in roots and shoots. The mutant plants revealed a decreased iron concentration in the shoots, and displayed severe leaf chlorosis under the condition of Fe limitation, compared to wild-type. Third, the product of GLU1, glutamate, could chelate iron in vivo and promote iron transportation. Last, we also found that supplementation of glutamate in the medium can alleviate cadmium toxicity in plants. Overall, our results provide evidence that GLU1 is involved in iron homeostasis through affecting glutamate synthesis under iron deficiency conditions in Arabidopsis.

An Update on Nitric Oxide Production and Role Under Phosphorus Scarcity in Plants

Phosphate (P) is characterized by its low availability and restricted mobility in soils, and also by a high redistribution capacity inside plants. In order to maintain P homeostasis in nutrient restricted conditions, plants have developed mechanisms which enable P acquisition from the soil solution, and an efficient reutilization of P already present in plant cells. Nitric oxide (NO) is a bioactive molecule with a plethora of functions in plants. Its endogenous synthesis depends on internal and environmental factors, and is closely tied with nitrogen (N) metabolism. Furthermore, there is evidence demonstrating that N supply affects P homeostasis and that P deficiency impacts on N assimilation. This review will provide an overview on how NO levels in planta are affected by P deficiency, the interrelationship with N metabolism, and a summary of the current understanding about the influence of this reactive N species over the processes triggered by P starvation, which could modify P use efficiency.

Ethylene Response Factors MbERF4 and MbERF72 Suppress Iron Uptake in Woody Apple Plants by Modulating Rhizosphere pH

Iron (Fe) deficiency limits the yield of fruit trees. When subjected to Fe deficiency, H+ secretion increases in the rhizosphere of dicotyledonous plants and pH decreases. This leads to the acidification of the soil and promotes Fe3+ to Fe2+ conversion, which plants can better uptake. This study investigated the relationship between two inhibitory transcription factors (ethylene response factors MbERF4 and MbERF72) and the H+-ATPase gene MbHA2. Two species of apple woody plants were studied: the Fe-inefficient Malus baccata and the Fe-efficient Malus xiaojinensis. Yeast one-hybrid and electrophoretic mobility shift assays showed that both MbERF4 and MbERF72 bind to the GCC cassette (AGCCGCC) of the MbHA2 promoter. Moreover, yeast two-hybrid and bimolecular fluorescence complementation assays showed that MbERF4 interacts with MbERF72. Furthermore, β-glucuronidase and luciferase reporter assays showed that the MbERF4- and MbERF72-induced repression of MbHA2 expression is synergistic. Virus-induced gene silencing of MbERF4 or MbERF72 increased MbHA2 expression, and thus lowered the rhizosphere pH in M. baccata. Consequently, the high expressions of MbERF4 and MbERF72 induced by Fe deficiency contributed to the Fe sensitivity of M. baccata. Moreover, the low expressions of MxERF4 and MxERF72 contributed to the Fe-deficiency tolerance of M. xiaojinensis via different binding conditions to the HA2 promoter. In summary, this study identified the relationship of two inhibitory transcription factors with the H+-ATPase gene and proposed a model in which ERF4 and ERF72 affect the rhizosphere pH in response to Fe deficiency.

Interactions Between Phosphorus, Zinc, and Iron Homeostasis in Nonmycorrhizal and Mycorrhizal Plants

Phosphorus (P), zinc (Zn), and iron (Fe) are three essential elements for plant survival, and severe deficiencies in these nutrients lead to growth retardation and crop yield reduction. This review synthesizes recent progress on how plants coordinate the acquisition and signaling of Pi, Zn, and Fe from surrounding environments and which genes are involved in these Pi-Zn-Fe interactions with the aim of better understanding of the cross-talk between these macronutrient and micronutrient homeostasis in plants. In addition, identification of genes important for interactions between Pi, Zn, and/or Fe transport and signaling is a useful target for breeders for improvement in plant nutrient acquisition. Furthermore, to understand these processes in arbuscular mycorrhizal plants, the preliminary examination of interactions between Pi, Zn, and Fe homeostasis in some relevant crop species has been performed at the physiological level and is summarized in this article. In conclusion, the development of integrative study of cross-talks between Pi, Zn, and Fe signaling pathway in mycorrhizal plants will be essential for sustainable agriculture all around the world.

Iron transport and its regulation in plants

Iron is an essential element for plants as well as other organisms, functioning in various cellular processes, including respiration, chlorophyll biosynthesis, and photosynthesis. Plants take up iron from soil in which iron solubility is extremely low especially under aerobic conditions at high-pH range. Therefore, plants have evolved efficient iron-uptake mechanisms. Because iron is prone to being precipitated and excess ionic iron is cytotoxic, plants also have sophisticated internal iron-transport mechanisms. These transport mechanisms comprise iron chelators including nicotianamine, mugineic acid family phytosiderophores and citrate, and various types of transporters of these chelators, iron-chelate complexes, or free iron ions. To maintain iron homeostasis, plants have developed mechanisms for regulating gene expression in response to iron availability. Expression of various genes involved in iron uptake and translocation is induced under iron deficiency by transcription factor networks and is negatively regulated by the ubiquitin ligase HRZ/BTS. This response is deduced to be mediated by cellular iron sensing as well as long-distance iron signaling. The ubiquitin ligase HRZ/BTS is a candidate intracellular iron sensor because it binds to iron and zinc, and its activity is affected by iron availability. The iron-excess response of plants is thought to be partially independent of the iron-deficiency response. In this review, we summarize and discuss extant knowledge of plant iron transport and its regulation.

The Altered Expression of microRNA408 Influences the Arabidopsis Response to Iron Deficiency

MicroRNAs contribute to the adaptation of plants to varying environmental conditions by affecting systemic mineral nutrient homeostasis. Copper and iron deficiencies antagonistically control the expression of Arabidopsis thaliana microRNA408 (miR408), which post-transcriptionally regulates laccase-like multicopper oxidase family members LAC3, LAC12, and LAC13. In this work, we used miR408 T-DNA insertion mutants (408-KO1 and 408-KO2) and a previously characterized transgenic line overexpressing miR408 (35S:408-14) to explore how miR408 influences copper- and iron-dependent metabolism. We observed that the altered expression of miR408 diminished plant performance and the activation of the iron-regulated genes under iron-deficient conditions. Consistently with the low expression of the miR408-target laccases, we showed that the vascular bundle lignification of the 35S:408-14 plants diminished. The decrease in the phenoloxidase and ferroxidase activities exhibited by wild-type plants under iron deficiency did not occur in the 408-KO1 plants, probably due to the higher expression of laccases. Finally, we observed that the hydrogen peroxide levels under iron starvation were altered in both the 408-KO1 and 35S:408-14 lines. Taken together, these results suggest that Arabidopsis plants with modified miR408 levels undergo multiple deregulations under iron-deficient conditions.

Understanding Fe2+ toxicity and P deficiency tolerance in rice for enhancing productivity under acidic soils

Plants experience low phosphorus (P) and high iron (Fe) levels in acidic lowland soils that lead to reduced crop productivity. A better understanding of the relationship between these two stresses at molecular and physiological level will lead to development of suitable strategies to increase crop productivity in such poor soils. Tolerance for most abiotic stresses including P deficiency and Fe toxicity is a quantitative trait in rice. Recent studies in the areas of physiology, genetics, and overall metabolic pathways in response to P deficiency of rice plants have improved our understanding of low P tolerance. Phosphorous uptake and P use efficiency are the two key traits for improving P deficiency tolerance. In the case of Fe toxicity tolerance, QTLs have been reported but the identity and role played by underlying genes is just emerging. Details pertaining to Fe deficiency tolerance in rice are well worked out including genes involved in Fe sensing and uptake. But, how rice copes with Fe toxicity is not clearly understood. This review focuses on the progress made in understanding these key environmental stresses. Finally, an opinion on the key genes which can be targeted for this stress is provided.

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.

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.

Integration of P, S, Fe, and Zn nutrition signals in Arabidopsis thaliana: potential involvement of PHOSPHATE STARVATION RESPONSE 1 (PHR1)

Phosphate and sulfate are essential macro-elements for plant growth and development, and deficiencies in these mineral elements alter many metabolic functions. Nutritional constraints are not restricted to macro-elements. Essential metals such as zinc and iron have their homeostasis strictly genetically controlled, and deficiency or excess of these micro-elements can generate major physiological disorders, also impacting plant growth and development. Phosphate and sulfate on one hand, and zinc and iron on the other hand, are known to interact. These interactions have been partly described at the molecular and physiological levels, and are reviewed here. Furthermore the two macro-elements phosphate and sulfate not only interact between themselves but also influence zinc and iron nutrition. These intricated nutritional cross-talks are presented. The responses of plants to phosphorus, sulfur, zinc, or iron deficiencies have been widely studied considering each element separately, and some molecular actors of these regulations have been characterized in detail. Although some scarce reports have started to examine the interaction of these mineral elements two by two, a more complex analysis of the interactions and cross-talks between the signaling pathways integrating the homeostasis of these various elements is still lacking. However, a MYB-like transcription factor, PHOSPHATE STARVATION RESPONSE 1, emerges as a common regulator of phosphate, sulfate, zinc, and iron homeostasis, and its role as a potential general integrator for the control of mineral nutrition is discussed.

Dynamics of long-distance signaling via plant vascular tissues

Plant vascular systems are constructed by specific cell wall modifications through which cells are highly specialized to make conduits for water and nutrients. Xylem vessels are formed by thickened cell walls that remain after programmed cell death, and serve as water conduits from the root to the shoot. In contrast, phloem tissues consist of a complex of living cells, including sieve tube elements and their neighboring companion cells, and translocate photosynthetic assimilates from mature leaves to developing young tissues. Intensive studies on the content of vascular flow fluids have unveiled that plant vascular tissues transport various types of gene product, and the transport of some provides the molecular basis for the long-distance communications. Analysis of xylem sap has demonstrated the presence of proteins in the xylem transpiration stream. Recent studies have revealed that CLE and CEP peptides secreted in the roots are transported to above ground via the xylem in response to plant-microbe interaction and soil nitrogen starvation, respectively. Their leucine-rich repeat transmembrane receptors localized in the shoot phloem are required for relaying the signal from the shoot to the root. These findings well-fit to the current scenario of root-to-shoot-to-root feedback signaling, where peptide transport achieves the root-to-shoot signaling, the first half of the signaling process. Meanwhile, it is now well-evidenced that proteins and a range of RNAs are transported via the phloem translocation system, and some of those can exert their physiological functions at their destinations, including roots. Thus, plant vascular systems may serve not only as conduits for the translocation of essential substances but also as long-distance communication pathways that allow plants to adapt to changes in internal and external environments at the whole plant level.

2'-Deoxymugineic acid promotes growth of rice (Oryza sativa L.) by orchestrating iron and nitrate uptake processes under high pH conditions

Poaceae plants release 2'-deoxymugineic acid (DMA) and related phytosiderophores to chelate iron (Fe), which often exists as insoluble Fe(III) in the rhizosphere, especially under high pH conditions. Although the molecular mechanisms behind the biosynthesis and secretion of DMA have been studied extensively, little information is known about whether DMA has biological roles other than chelating Fe in vivo. Here, we demonstrate that hydroponic cultures of rice (Oryza sativa) seedlings show almost complete restoration in shoot height and soil-plant analysis development (SPAD) values after treatment with 3-30 μm DMA at high pH (pH 8.0), compared with untreated control seedlings at normal pH (pH 5.8). These changes were accompanied by selective accumulation of Fe over other metals. While this enhanced growth was evident under high pH conditions, DMA application also enhanced seedling growth under normal pH conditions in which Fe was fairly accessible. Microarray and qRT-PCR analyses revealed that exogenous DMA application attenuated the increased expression levels of various genes related to Fe transport and accumulation. Surprisingly, despite the preferential utilization of ammonium over nitrate as a nitrogen source by rice, DMA application also increased nitrate reductase activity and the expression of genes encoding high-affinity nitrate transporters and nitrate reductases, all of which were otherwise considerably lower under high pH conditions. These data suggest that exogenous DMA not only plays an important role in facilitating the uptake of environmental Fe, but also orchestrates Fe and nitrate assimilation for optimal growth under high pH conditions.

Iron deficiency responses in rice roots

Iron (Fe) is an essential element for most living organisms. To acquire sparingly soluble Fe from the rhizosphere, rice roots rely on two Fe acquisition pathways. The first of these pathways involves Fe(III) chelators specific to graminaceous plants, the mugineic acid family phytosiderophores, and the second involves absorption of Fe(2+). Key components in this response include enzymes involved in the biosynthesis of deoxymugineic acid (OsNAS1, OsNAS2, OsNAAT1, and OsDMAS1), the deoxymugineic acid efflux transporter (TOM1), the Fe(III)-deoxymugineic acid transporter (OsYSL15), and Fe(2+) transporters (OsIRT1, OsIRT2, and OsNRAMP1). In whole roots, these proteins are expressed in a coordinated manner with strong transcriptional induction in response to Fe deficiency. Radial transport of Fe to xylem and phloem is also mediated by the mugineic acid family phytosiderophores, as well as other chelators and their transporters, including Fe(II)-nicotianamine transporter (OsYSL2), phenolics efflux transporters (PEZ1 and PEZ2), and citrate efflux transporter (OsFRDL1). Among these, OsYSL2 is strongly induced under conditions of Fe deficiency. Both transcriptional induction and potential feedback repression mediate the expressional regulation of the genes involved in Fe uptake and translocation in response to Fe deficiency. The transcription factors IDEF1, IDEF2, and OsIRO2 are responsible for transcriptional induction, whereas the ubiquitin ligases OsHRZ1 and OsHRZ2, as well as the transcription factors OsIRO3 and OsbHLH133, are thought to mediate negative regulation. Furthermore, IDEF1 and OsHRZs bind Fe and other metals, and are therefore candidate Fe sensors. The interacting functions of these regulators are thought to fine tune the expression of proteins involved in Fe uptake and translocation.

Iron sensors and signals in response to iron deficiency

The transcription of genes involved in iron acquisition in plants is induced under iron deficiency, but our understanding of iron sensors and signals remains limited. Iron Deficiency-responsive Element-binding Factor 1 (IDEF1) and Hemerythrin motif-containing Really Interesting New Gene- and Zinc-finger proteins (HRZs)/BRUTUS (BTS) have recently emerged as candidate iron sensors because of their functions as potent regulators of iron deficiency responses and their iron-binding properties. IDEF1 is a central transcriptional regulator of graminaceous genes involved in iron uptake and utilization, predominantly during the early stages of iron deficiency. HRZs/BTS are E3 ubiquitin ligases and negative regulators of iron deficiency responses in both graminaceous and non-graminaceous plants. Rice OsHRZ1 and OsHRZ2 are also potent regulators of iron accumulation. Characterizing these putative iron sensors also provides clues to understanding the nature of iron signals, which may involve ionized iron itself, other metals, oxygen, redox status, heme and iron-sulfur clusters, in addition to metabolites affected by iron deficiency. Systemic iron responses may also be regulated by phloem-mobile iron and its chelators such as nicotianamine. Iron sensors and signals will be identified by demonstration of signal transmission by IDEF1, HRZs/BTS, or unknown factors.

Comprehensive transcriptome analysis unravels the existence of crucial genes regulating primary metabolism during adventitious root formation in Petunia hybrida

To identify specific genes determining the initiation and formation of adventitious roots (AR), a microarray-based transcriptome analysis in the stem base of the cuttings of Petunia hybrida (line W115) was conducted. A microarray carrying 24,816 unique, non-redundant annotated sequences was hybridized to probes derived from different stages of AR formation. After exclusion of wound-responsive and root-regulated genes, 1,354 of them were identified which were significantly and specifically induced during various phases of AR formation. Based on a recent physiological model distinguishing three metabolic phases in AR formation, the present paper focuses on the response of genes related to particular metabolic pathways. Key genes involved in primary carbohydrate metabolism such as those mediating apoplastic sucrose unloading were induced at the early sink establishment phase of AR formation. Transcriptome changes also pointed to a possible role of trehalose metabolism and SnRK1 (sucrose non-fermenting 1- related protein kinase) in sugar sensing during this early step of AR formation. Symplastic sucrose unloading and nucleotide biosynthesis were the major processes induced during the later recovery and maintenance phases. Moreover, transcripts involved in peroxisomal beta-oxidation were up-regulated during different phases of AR formation. In addition to metabolic pathways, the analysis revealed the activation of cell division at the two later phases and in particular the induction of G1-specific genes in the maintenance phase. Furthermore, results point towards a specific demand for certain mineral nutrients starting in the recovery phase.

Analysis of the Root System Architecture of Arabidopsis Provides a Quantitative Readout of Crosstalk between Nutritional Signals

As plant roots forage the soil for food and water, they translate a multifactorial input of environmental stimuli into a multifactorial developmental output that manifests itself as root system architecture (RSA). Our current understanding of the underlying regulatory network is limited because root responses have traditionally been studied separately for individual nutrient deficiencies. In this study, we quantified 13 RSA parameters of Arabidopsis thaliana in 32 binary combinations of N, P, K, S, and light. Analysis of variance showed that each RSA parameter was determined by a typical pattern of environmental signals and their interactions. P caused the most important single-nutrient effects, while N-effects were strongly light dependent. Effects of K and S occurred mostly through nutrient interactions in paired or multiple combinations. Several RSA parameters were selected for further analysis through mutant phenotyping, which revealed combinations of transporters, receptors, and kinases acting as signaling modules in K-N interactions. Furthermore, nutrient response profiles of individual RSA features across NPK combinations could be assigned to transcriptionally coregulated clusters of nutrient-responsive genes in the roots and to ionome patterns in the shoots. The obtained data set provides a quantitative basis for understanding how plants integrate multiple nutritional stimuli into complex developmental programs.

The genetic basis of natural variation for iron homeostasis in the maize IBM population

BACKGROUND

Iron (Fe) deficiency symptoms in maize (Zea mays subsp. mays) express as leaf chlorosis, growth retardation, as well as yield reduction and are typically observed when plants grow in calcareous soils at alkaline pH. To improve our understanding of genotypical variability in the tolerance to Fe deficiency-induced chlorosis, the objectives of this study were to (i) determine the natural genetic variation of traits related to Fe homeostasis in the maize intermated B73 × Mo17 (IBM) population, (ii) to identify quantitative trait loci (QTLs) for these traits, and (iii) to analyze expression levels of genes known to be involved in Fe homeostasis as well as of candidate genes obtained from the QTL analysis.

RESULTS

In hydroponically-grown maize, a total of 47 and 39 QTLs were detected for the traits recorded under limited and adequate supply of Fe, respectively.

CONCLUSIONS

From the QTL results, we were able to identify new putative candidate genes involved in Fe homeostasis under a deficient or adequate Fe nutritional status, like Ferredoxin class gene, putative ferredoxin PETF, metal tolerance protein MTP4, and MTP8. Furthermore, our expression analysis of candidate genes suggested the importance of trans-acting regulation for 2'-deoxymugineic acid synthase 1 (DMAS1), nicotianamine synthase (NAS3, NAS1), formate dehydrogenase 1 (FDH1), methylthioribose-1-phosphate isomerase (IDI2), aspartate/tyrosine/aromatic aminotransferase (IDI4), and methylthioribose kinase (MTK).

Iron speciation in the cytosol: an overview

The nature of the cytosolic iron pool remains largely uncharacterized, although a range of candidate ligands and chaperones have been proposed. Herein an overview is presented of cytosolic non heme and non iron-sulphur cluster protein iron binding sites and the influence of ligands on the redox activity of iron. This analysis leads to the concept of iron(II) glutathione functioning as the labile cytosolic iron pool and offers a means for the selection of iron over manganese in subsequent incorporation into a wide range of iron-dependent enzymes and electron transfer proteins. Glutathione and glutathione-binding glutaredoxins play a critical role in iron sulfur cluster synthesis and Fe(II)GS (iron(II) coordinated by the thiol function of glutathione) is a suitable iron donor for this biosynthetic route. Significantly, both glutathione and glutaredoxins are universally distributed and thus a controlling influence of glutathione on intracellular iron trafficking is likely to be a common feature of the majority of living organisms.

Fine regulation of leaf iron use efficiency and iron root uptake under limited iron bioavailability

Numerous studies have investigated the molecular and physiological-morphological mechanisms induced in plant roots in response to specific nutrient deficiencies. Both transcriptional and post-transcriptional mechanisms are involved that increase root uptake under nutrient deficiency. Root nutrient deficiency-stress root responses are mainly regulated by the nutrient status in the shoot. The signals involved in shoot to root cross-talk regulation processes for the activation of nutrient-deficiency induced root responses are not clearly elucidated. The physiological-molecular events in the leaf linked to the nutrient availability for metabolic use, are also poorly known. In this context, we focus our attention on iron plant nutrition. Some experimental evidence suggests the existence of a regulatory system concerned with the optimization of the metabolic use of iron, mainly under conditions of iron starvation. This system seems to be activated by the deficiency in iron-availability for metabolic processes in the leaf and regulates the activation of some iron-stress root responses. This regulation seems to be probably expressed by affecting the production and/or translocation of the activating signal sent from the shoot to the root under conditions of iron deficiency in the shoot.

MicroRNAs play critical roles during plant development and in response to abiotic stresses

MicroRNAs (miRNAs) have been identified as key molecules in regulatory networks. The fine-tuning role of miRNAs in addition to the regulatory role of transcription factors has shown that molecular events during development are tightly regulated. In addition, several miRNAs play crucial roles in the response to abiotic stress induced by drought, salinity, low temperatures, and metals such as aluminium. Interestingly, several miRNAs have overlapping roles with regard to development, stress responses, and nutrient homeostasis. Moreover, in response to the same abiotic stresses, different expression patterns for some conserved miRNA families among different plant species revealed different metabolic adjustments. The use of deep sequencing technologies for the characterisation of miRNA frequency and the identification of new miRNAs adds complexity to regulatory networks in plants. In this review, we consider the regulatory role of miRNAs in plant development and abiotic stresses, as well as the impact of deep sequencing technologies on the generation of miRNA data.

Effects of the coordination mechanism between roots and leaves induced by root-breaking and exogenous cytokinin spraying on the grazing tolerance of ryegrass

The grazing tolerance mechanism of ryegrass was investigated by examining the effects of roots on leaves under frequent defoliation. The study consisted of four treatments: (1) with root breaking and cytokinin spraying, (2) root breaking without cytokinin spraying, (3) cytokinin spraying with no root breaking, and (4) no root breaking and no cytokinin spraying. Results showed that root breaking or frequent defoliation inhibited the ryegrass regrowth, which resulted in low biomass of the newly grown leaves and roots, as well as low soluble carbohydrate content and xylem sap quantity in the roots. Spraying with exogenous cytokinin promoted the increase in newly grown leaf biomass, but decreased root biomass, root soluble carbohydrate content, and root xylem sap quantity. Determination of gibberellic acid, indole-3-acetic acid, abscisic acid, and zeatin riboside (ZR) in roots, newly grown leaves, and stubbles showed that cytokinin is a key factor in ryegrass regrowth under frequent defoliation. Root breaking and frequent defoliation both decreased the ZR content in roots and in newly grown leaves, whereas spraying with exogenous cytokinin increased the ZR content in roots and in newly grown leaves. Therefore, cytokinin enhances the above ground productivity at the cost of root growth under frequent defoliation.

Iron uptake, translocation, and regulation in higher plants

Iron is essential for the survival and proliferation of all plants. Higher plants have developed two distinct strategies to acquire iron, which is only slightly soluble, from the rhizosphere: the reduction strategy of nongraminaceous plants and the chelation strategy of graminaceous plants. Key molecular components-including transporters, enzymes, and chelators-have been clarified for both strategies, and many of these components are now thought to also function inside the plant to facilitate internal iron transport. Transporters for intracellular iron trafficking are also being clarified. A majority of genes encoding these components are transcriptionally regulated in response to iron availability. Recent research has uncovered central transcription factors, cis-acting elements, and molecular mechanisms regulating these genes. Manipulation of these molecular components has produced transgenic crops with enhanced tolerance to iron deficiency or with increased iron content in the edible parts.

Use of natural variation reveals core genes in the transcriptome of iron-deficient Arabidopsis thaliana roots

Iron (Fe) is an essential mineral micronutrient for plants and animals. Plants respond to Fe deficiency by increasing root uptake capacity. Identification of gene networks for Fe uptake and homeostasis could result in improved crop growth and nutritional value. Previous studies have used microarrays to identify a large number of genes regulated by Fe deficiency in roots of three Arabidopsis ecotypes. However, a large proportion of these genes may be involved in secondary or genotype-influenced responses rather than in a universal role in Fe uptake or homeostasis. Here we show that a small percentage of the Fe deficiency transcriptome of two contrasting ecotypes, Kas-1 and Tsu-1, was shared with other ecotypes. Kas-1 and Tsu-1 had different timing and magnitude of ferric reductase activity upon Fe withdrawal, and different categories of overrepresented Fe-regulated genes. To gain insights into universal responses of Arabidopsis to Fe deficiency, the Kas-1 and Tsu-1 transcriptomes were compared with those of Col-0, Ler, and C24. In early Fe deficiency (24-48 h), no Fe-downregulated genes and only 10 upregulated genes were found in all ecotypes, and only 20 Fe-downregulated and 58 upregulated genes were found in at least three of the five ecotypes. Supernode gene networks were constructed to visualize conserved Fe homeostasis responses. Contrasting gene expression highlighted different responses to Fe deficiency between ecotypes. This study demonstrates the use of natural variation to identify central Fe-deficiency-regulated genes in plants, and identified genes with potential new roles in signalling during Fe deficiency.

Fitting into the harsh reality: regulation of iron-deficiency responses in dicotyledonous plants

Iron is an essential element for life on Earth and its shortage, or excess, in the living organism may lead to severe health disorders. Plants serve as the primary source of dietary iron and improving crop iron content is an important step towards a better public health. Our review focuses on the control of iron acquisition in dicotyledonous plants and monocots that apply a reduction-based strategy in order to mobilize and import iron from the rhizosphere. Achieving a balance between shortage and excess of iron requires a tight regulation of the activity of the iron uptake system. A number of studies, ranging from single gene characterization to systems biology analyses, have led to the rapid expansion of our knowledge on iron uptake in recent years. Here, we summarize the novel insights into the regulation of iron acquisition and internal mobilization from intracellular stores. We present a detailed view of the main known regulatory networks defined by the Arabidopsis regulators FIT and POPEYE (PYE). Additionally, we analyze the root and leaf iron-responsive regulatory networks, revealing novel potential gene interactions and reliable iron-deficiency marker genes. We discuss perspectives and open questions with regard to iron sensing and post-translational regulation.

Localized iron supply triggers lateral root elongation in Arabidopsis by altering the AUX1-mediated auxin distribution

Root system architecture depends on nutrient availability, which shapes primary and lateral root development in a nutrient-specific manner. To better understand how nutrient signals are integrated into root developmental programs, we investigated the morphological response of Arabidopsis thaliana roots to iron (Fe). Relative to a homogeneous supply, localized Fe supply in horizontally separated agar plates doubled lateral root length without having a differential effect on lateral root number. In the Fe uptake-defective mutant iron-regulated transporter1 (irt1), lateral root development was severely repressed, but a requirement for IRT1 could be circumvented by Fe application to shoots, indicating that symplastic Fe triggered the local elongation of lateral roots. The Fe-stimulated emergence of lateral root primordia and root cell elongation depended on the rootward auxin stream and was accompanied by a higher activity of the auxin reporter DR5-β-glucuronidase in lateral root apices. A crucial role of the auxin transporter AUXIN RESISTANT1 (AUX1) in Fe-triggered lateral root elongation was indicated by Fe-responsive AUX1 promoter activities in lateral root apices and by the failure of the aux1-T mutant to elongate lateral roots into Fe-enriched agar patches. We conclude that a local symplastic Fe gradient in lateral roots upregulates AUX1 to accumulate auxin in lateral root apices as a prerequisite for lateral root elongation.

Chloroplastic and mitochondrial metal homeostasis

Transition metal deficiency has a strong impact on the growth and survival of an organism. Indeed, transition metals, such as iron, copper, manganese and zinc, constitute essential cofactors for many key cellular functions. Both photosynthesis and respiration rely on metal cofactor-mediated electron transport chains. Chloroplasts and mitochondria are, therefore, organelles with high metal ion demand and represent essential components of the metal homeostasis network in photosynthetic cells. In this review, we describe the metal requirements of chloroplasts and mitochondria, the acclimation of their functions to metal deficiency and recent advances in our understanding of their contributions to cellular metal homeostasis, the control of the cellular redox status and the synthesis of metal cofactors.

Towards a knowledge-based correction of iron chlorosis

Iron (Fe) deficiency-induced chlorosis is a major nutritional disorder in crops growing in calcareous soils. Iron deficiency in fruit tree crops causes chlorosis, decreases in vegetative growth and marked fruit yield and quality losses. Therefore, Fe fertilizers, either applied to the soil or delivered to the foliage, are used every year to control Fe deficiency in these crops. On the other hand, a substantial body of knowledge is available on the fundamentals of Fe uptake, long and short distance Fe transport and subcellular Fe allocation in plants. Most of this basic knowledge, however, applies only to Fe deficiency, with studies involving Fe fertilization (i.e., with Fe-deficient plants resupplied with Fe) being still scarce. This paper reviews recent developments in Fe-fertilizer research and the state-of-the-art of the knowledge on Fe acquisition, transport and utilization in plants. Also, the effects of Fe-fertilization on the plant responses to Fe deficiency are reviewed. Agronomical Fe-fertilization practices should benefit from the basic knowledge on plant Fe homeostasis already available; this should be considered as a long-term goal that can optimize fertilizer inputs, reduce grower's costs and minimize the environmental impact of fertilization.

Moving micronutrients from the soil to the seeds: genes and physiological processes from a biofortification perspective

The micronutrients iron (Fe), zinc (Zn), and copper (Cu) are essential for plants and the humans and animals that consume plants. Increasing the micronutrient density of staple crops, or biofortification, will greatly improve human nutrition on a global scale. This review discusses the processes and genes needed to translocate micronutrients through the plant to the developing seeds, and potential strategies for developing biofortified crops.

Ethylene is involved in the regulation of iron homeostasis by regulating the expression of iron-acquisition-related genes in Oryza sativa

Plants employ two distinct strategies to obtain iron (Fe) from the soil. In Strategy I but not Strategy II plants, Fe limitation invokes ethylene production which regulates Fe deficiency responses. Oryza sativa (rice) is the only graminaceous plant described that possesses a Strategy I-like system for iron uptake as well as the classic Strategy II system. Ethylene production of rice roots was significantly increased when grown under Fe-depleted conditions. Moreover, 1-aminocyclopropane-1-carboxylic acid (ACC) treatment, a precursor of ethylene, conferred tolerance to Fe deficiency in rice by increasing internal Fe availability. Gene expression analysis of rice iron-regulated bHLH transcription factor OsIRO2, nicotianamine synthases 1 and 2 (NAS1 and NAS2), yellow-stripe like transporter 15 (YSL15) and iron-regulated transporter (IRT1) indicated that ethylene caused an increase in transcript abundance of both Fe (II) and Fe (III)-phytosiderophore uptake systems. RNA interference of OsIRO2 in transgenic rice showed that ethylene acted via this transcription factor to induce the expression of OsNAS1, OsNAS2, OsYSL15, and OsIRT1. By contrast, in Hordeum vulgare L. (barley), no ethylene production or ethylene-mediated effects of Fe response could be detected. In conclusion, Fe-limiting conditions increased ethylene production and signalling in rice, which is novel in Strategy II plant species.

Chemistry and biology of siderophores

Siderophores are compounds produced by bacteria, fungi and graminaceous plants for scavenging iron from the environment. They are low-molecular-weight compounds (500-1500 daltons) possessing a high affinity for iron(III) (Kf > 1030), the biosynthesis of which is regulated by iron levels and the function of which is to supply iron to the cell. This article briefly describes the classification and chemical properties of siderophores, before outlining research on siderophore biosynthesis and transport. Clinically important siderophores and the therapeutic potential of siderophore design are described. Appendix 1 provides a comprehensive list of siderophore structures.

General regulatory patterns of plant mineral nutrient depletion as revealed by serat quadruple mutants disturbed in cysteine synthesis

Sulfate is an essential macronutrient for plants. Plants have developed strategies to cope with sulfate deficiency, and other nutrient ion limitations. However, the regulation of these adaptive responses and the coordinating signals that underlie them are still poorly characterized. O-acetylserine (OAS) is a marker metabolite of sulfate starvation and has been speculated to have a signaling function. OAS is synthesized by the enzyme serine acetyltransferase (SERAT), which is encoded by five distinct genes in Arabidopsis. We investigated quadruple knockout mutants of SERAT that retained only one functional isoform. These mutants displayed symptoms of sulfate starvation. Furthermore, some of them displayed phenotypes typical of prolonged sulfate starvation, in particular, developmental programs associated with senescence or stress responses. Thus, we compared metabolite and transcriptome data from these mutants with N-, P-, K-, and S-depleted plants. This revealed many similarities with general nutrient-depletion-induced senescence (NuDIS), indicating the recruitment of existing regulatory programs for nutrient-starvation responses. Several candidate genes that could be involved in these processes were identified, including transcription factors and other regulatory proteins, as well as the functional categories of their target genes. These results outline components of the regulatory network controlling plant development under sulfate stress, forming a basis for further investigations to elucidate the complete network. In turn, this will advance our broader understanding of plant responses to a range of other nutrient stresses.

Recent insights into iron homeostasis and their application in graminaceous crops

Higher plants utilize various mechanisms to maintain iron homeostasis. To acquire sparingly soluble iron from the rhizosphere, graminaceous plants synthesize natural iron (III) chelators known as mugineic acid family phytosiderophores (MAs). Recent research has uncovered various genes involved in iron uptake and translocation, as well as factors regulating the expression of these genes, especially in rice. Manipulation of these molecular components is used to produce transgenic crops with enhanced tolerance to iron deficiency, or with a high seed iron content. Since iron homeostasis is closely linked to that of other mineral elements, an understanding of this phenomenon will serve as the basis for the production of crops with low concentrations of toxic metals and transgenic plants for phytoremediation.