Rice genes involved in phytosiderophore biosynthesis are synchronously regulated during the early stages of iron deficiency in roots

Deciphering the regulation of transporters and mitogen-activated protein kinase in arsenic and iron exposed rice

This study investigates the influence of arsenic (As) and iron (Fe) on the molecular aspects of rice plants. The mRNA-abundance of As (OsLsi, OsPHT, OsNRAMP1, OsABCC1) and Fe (OsIRT, OsNRAMP1, OsYSL, OsFRDL1, OsVIT2, OsSAMS1, OsNAS, OsNAAT1, OsDMAS1, OsTOM1, OsFER) related genes has been observed in 12-d old As and Fe impacted rice varieties. Analyses of phytosiderophores synthesis and Fe-uptake genes affirm the existence of specialized Fe-uptake strategies in rice with varieties PB-1 and Varsha favouring strategy I and II, respectively. Expression of OsNAS3, OsVIT2, OsFER and OsABCC1 indicated PB-1's tolerance towards Fe and As. Analysis of mitogen-activated protein kinase cascade members (OsMKK3, OsMKK4, OsMKK6, OsMPK3, OsMPK4, OsMPK7, and OsMPK14) revealed their importance in the fine adjustment of As/Fe in the rice system. A conditional network map was generated based on the gene expression pattern that unfolded the differential dynamics of both rice varieties. The mating based split ubiquitin system determined the interaction of OsIRT1 with OsMPK3, and OsLsi1 with both OsMPK3 and OsMPK4. In-silico tools also confirmed the binding affinities of OsARM1 with OsLsi1, OsMPK3 and OsMPK4, and of OsIDEF1/OsIRO2 with OsIRT1 and OsMPK3, supporting our hypothesis that OsARM1, OsIDEF1, OsIRO2 were active in the connections discovered by mbSUS.

Silicon and iron nanoparticles protect rice against lead (Pb) stress by improving oxidative tolerance and minimizing Pb uptake

Lead (Pb) is toxic to the development and growth of rice plants. Nanoparticles (NPs) have been considered one of the efficient remediation techniques to mitigate Pb stress in plants. Therefore, a study was carried out to examine the underlying mechanism of iron (Fe) and silicon (Si) nanoparticle-induced Pb toxicity alleviation in rice seedlings. Si-NPs (2.5 mM) and Fe-NPs (25 mg L-1) were applied alone and in combination to rice plants grown without (control; no Pb stress) and with (100 µM) Pb concentration. Our results revealed that Pb toxicity severely affected all rice growth-related traits, such as inhibited root fresh weight (42%), shoot length (24%), and chlorophyll b contents (26%). Moreover, a substantial amount of Pb was translocated to the above-ground parts of plants, which caused a disturbance in the antioxidative enzyme activities. However, the synergetic use of Fe- and Si-NPs reduced the Pb contents in the upper part of plants by 27%. It reduced the lethal impact of Pb on roots and shoots growth parameters by increasing shoot length (40%), shoot fresh weight (48%), and roots fresh weight (31%). Both Si and Fe-NPs synergistic application significantly elevated superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and glutathione (GSH) concentrations by 114%, 186%, 135%, and 151%, respectively, compared to plants subjected to Pb stress alone. The toxicity of Pb resulted in several cellular abnormalities and altered the expression levels of metal transporters and antioxidant genes. We conclude that the synergistic application of Si and Fe-NPs can be deemed favorable, environmentally promising, and cost-effective for reducing Pb deadliness in rice crops and reclaiming Pb-polluted soils.

Effect of the Nonpathogenic Strain Fusarium oxysporum FO12 on Fe Acquisition in Rice (Oryza sativa L.) Plants

Rice (Oryza sativa L.) is a very important cereal worldwide, since it is the staple food for more than half of the world's population. Iron (Fe) deficiency is among the most important agronomical concerns in calcareous soils where rice plants may suffer from this deficiency. Current production systems are based on the use of high-yielding varieties and the application of large quantities of agrochemicals, which can cause major environmental problems. The use of beneficial rhizosphere microorganisms is considered a relevant sustainable alternative to synthetic fertilizers. The main goal of this study was to determine the ability of the nonpathogenic strain Fusarium oxysporum FO12 to induce Fe-deficiency responses in rice plants and its effects on plant growth and Fe chlorosis. Experiments were carried out under hydroponic system conditions. Our results show that the root inoculation of rice plants with FO12 promotes the production of phytosiderophores and plant growth while reducing Fe chlorosis symptoms after several days of cultivation. Moreover, Fe-related genes are upregulated by FO12 at certain times in inoculated plants regardless of Fe conditions. This microorganism also colonizes root cortical tissues. In conclusion, FO12 enhances Fe-deficiency responses in rice plants, achieves growth promotion, and reduces Fe chlorosis symptoms.

Biofortification of Crops to Fight Anemia: Role of Vacuolar Iron Transporters

Plant-based foods provide all the crucial nutrients for human health. Among these, iron (Fe) is one of the essential micronutrients for plants and humans. A lack of Fe is a major limiting factor affecting crop quality, production, and human health. There are people who suffer from various health problems due to the low intake of Fe in their plant-based foods. Anemia has become a serious public health issue due to Fe deficiency. Enhancing Fe content in the edible part of food crops is a major thrust area for scientists worldwide. Recent progress in nutrient transporters has provided an opportunity to resolve Fe deficiency or nutritional problems in plants and humans. Understanding the structure, function, and regulation of Fe transporters is essential to address Fe deficiency in plants and to improve Fe content in staple food crops. In this review, we summarized the role of Fe transporter family members in the uptake, cellular and intercellular movement, and long-distance transport of Fe in plants. We draw insights into the role of vacuolar membrane transporters in the crop for Fe biofortification. We also provide structural and functional insights into cereal crops' vacuolar iron transporters (VITs). This review will help highlight the importance of VITs for improving the Fe biofortification of crops and alleviating Fe deficiency in humans.

Challenges and opportunities to regulate mineral transport in rice

Iron (Fe) is an essential mineral for plants, and its deficiency as well as toxicity severely affects plant growth and development. Although Fe is ubiquitous in mineral soils, its acquisition by plants is difficult to regulate particularly in acidic and alkaline soils. Under alkaline conditions, where lime is abundant, Fe and other mineral elements are sparingly soluble. In contrast, under low pH conditions, especially in paddy fields, Fe toxicity could occur. Fe uptake is complicated and could be integrated with copper (Cu), manganese (Mn), zinc (Zn), and cadmium (Cd) uptake. Plants have developed sophisticated mechanisms to regulate the Fe uptake from soil and its transport to root and above-ground parts. Here, we review recent developments in understanding metal transport and discuss strategies to effectively regulate metal transport in plants with a particular focus on rice.

Genome-Wide Identification of Wheat ZIP Gene Family and Functional Characterization of the TaZIP13-B in Plants

The ZIP (Zn-regulated, iron-regulated transporter-like protein) transporter plays an important role in regulating the uptake, transport, and accumulation of microelements in plants. Although some studies have identified ZIP genes in wheat, the significance of this family is not well understood, particularly its involvement under Fe and Zn stresses. In this study, we comprehensively characterized the wheat ZIP family at the genomic level and performed functional verification of three TaZIP genes by yeast complementary analysis and of TaZIP13-B by transgenic Arabidopsis. Totally, 58 TaZIP genes were identified based on the genome-wide search against the latest wheat reference (IWGSC_V1.1). They were then classified into three groups, based on phylogenetic analysis, and the members within the same group shared the similar exon-intron structures and conserved motif compositions. Expression pattern analysis revealed that the most of TaZIP genes were highly expressed in the roots, and nine TaZIP genes displayed high expression at grain filling stage. When exposed to ZnSO₄ and FeCl₃ solutions, the TaZIP genes showed differential expression patterns. Additionally, six ZIP genes responded to zinc-iron deficiency. A total of 57 miRNA-TaZIP interactions were constructed based on the target relationship, and three miRNAs were downregulated when exposed to the ZnSO₄ and FeCl₃ stresses. Yeast complementation analysis proved that TaZIP14-B, TaZIP13-B, and TaIRT2-A could transport Zn and Fe. Finally, overexpression of TaZIP13-B in Arabidopsis showed that the transgenic plants displayed better tolerance to Fe/Zn stresses and could enrich more metallic elements in their seeds than wild-type Arabidopsis. This study systematically analyzed the genomic organization, gene structure, expression profiles, regulatory network, and the biological function of the ZIP family in wheat, providing better understanding of the regulatory roles of TaZIPs and contributing to improve nutrient quality in wheat crops.

Iron oxide nanoparticles alleviate arsenic phytotoxicity in rice by improving iron uptake, oxidative stress tolerance and diminishing arsenic accumulation

The food chain contaminated with arsenic (As) has developed a hazardous threat to the growth and development of plants, animals and humans. The present study was conducted to examine the application of iron oxide nanoparticles (FeNPs) on biochemical and molecular traits of roots and leaves of rice plants under As phytotoxicity. The results showed that As reduced the accumulation of Fe in roots and leaves and thus reduced photosynthetic pigments and growth of rice plants. As stress enhanced the accumulation of hydrogen peroxide, superoxide anion and methylglyoxal by increasing the accumulation of As in roots and leaves, resulting in damage to membrane lipids and raised electrolyte leakage (EL). However, FeNPs strengthen the glyoxalase system and antioxidant enzymes, thereby alleviating oxidative stress and reducing EL. FeNPs protected plant cells from As phytotoxicity by enhancing the accumulation of chelating agents (proline, glutathione and phytochelatins) and the sequestration and immobilization of As in the vacuoles and the cell walls. FeNPs downregulated the expression of genes involved in As uptake and translocation (Lsi1 and Lsi2) and, consequently, reduced As accumulation in the roots and leaves of As-stressed plants. FeNPs also improved the accumulation of Fe in the roots and leaves by modulating the expression of genes that regulate Fe uptake and its transport to leaves (IRT1, IRT2, YSL2, YSL13, FRDL1, DMAS1, NAS2 and NAS3), resulting in the restoration of photosynthetic pigments and the growth of As-stressed plants. Our findings authenticate the role of FeNPs in diminishing As phytotoxicity on rice.

Iron deficiency-inducible peptide-coding genes OsIMA1 and OsIMA2 positively regulate a major pathway of iron uptake and translocation in rice

Under low iron (Fe) availability, plants transcriptionally induce various genes responsible for Fe uptake and translocation to obtain adequate amounts of Fe. Although transcription factors and ubiquitin ligases involved in these Fe deficiency responses have been identified, the mechanisms coordinating these pathways have not been clarified in rice. Recently identified Fe-deficiency-inducible IRON MAN (IMA)/FE UPTAKE-INDUCING PEPTIDE (FEP) positively regulates many Fe-deficiency-inducible genes for Fe uptake in Arabidopsis. Here, we report that the expression of two IMA/FEP genes in rice, OsIMA1 and OsIMA2, is strongly induced under Fe deficiency, positively regulated by the transcription factors IDEF1, OsbHLH058, and OsbHLH059, as well as OsIMA1 and OsIMA2 themselves, and negatively regulated by HRZ ubiquitin ligases. Overexpression of OsIMA1 or OsIMA2 in rice conferred tolerance to Fe deficiency and accumulation of Fe in leaves and seeds. These OsIMA-overexpressing rice exhibited enhanced expression of all of the known Fe-deficiency-inducible genes involved in Fe uptake and translocation, except for OsYSL2, a Fe-nicotianamine transporter gene, in roots but not in leaves. Knockdown of OsIMA1 or OsIMA2 caused minor effects, including repression of some Fe uptake- and translocation-related genes in OsIMA1 knockdown roots. These results indicate that OsIMA1 and OsIMA2 play key roles in enhancing the major pathway of the Fe deficiency response in rice.

Defects in the rice aconitase-encoding OsACO1 gene alter iron homeostasis

Rice aconitase gene OsACO1 is involved in the iron deficiency-signaling pathway for the expression of iron deficiency-inducible genes, either thorough enzyme activity or possible specific RNA binding for post-transcriptional regulation. Iron (Fe) is an essential element for virtually all living organisms. When plants are deficient in Fe, Fe acquisition systems are activated to maintain Fe homeostasis, and this regulation is mainly executed at the gene transcription level. Many molecules responsible for Fe uptake, translocation, and storage in plants have been identified and characterized. However, how plants sense Fe status within cells and then induce a transcriptional response is still unclear. In the present study, we found that knockdown of the OsACO1 gene, which encodes an aconitase in rice, leads to the down-regulation of selected Fe deficiency-inducible genes involved in Fe uptake and translocation in roots, and a decrease in Fe concentration in leaves, even when grown under Fe-sufficient conditions. OsACO1 knockdown plants showed a delayed transcriptional response to Fe deficiency compared to wild-type plants. In contrast, overexpression of OsACO1 resulted in the opposite effects. These results suggest that OsACO1 is situated upstream of the Fe deficiency-signaling pathway. Furthermore, we found that the OsACO1 protein potentially has RNA-binding activity. In vitro screening of RNA interactions with OsACO1 revealed that RNA potentially forms a unique stem-loop structure that interacts with OsACO1 via a conserved GGUGG motif within the loop structure. These results suggest that OsACO1 regulate Fe deficiency response either thorough enzyme activity catalyzing isomerization of citrate, or specific RNA binding for post-transcriptional regulation.

The Molecular Mechanisms Underlying Iron Deficiency Responses in Rice

Iron (Fe) is an essential element required for plant growth and development. Under Fe-deficientconditions, plants have developed two distinct strategies (designated as strategy I and II) to acquire Fe from soil. As a graminaceous species, rice is not a typical strategy II plant, as it not only synthesizes DMA (2'-deoxymugineic acid) in roots to chelate Fe3+ but also acquires Fe2+ through transporters OsIRT1 and OsIRT2. During the synthesis of DMA in rice, there are three sequential enzymatic reactions catalyzed by enzymes NAS (nicotianamine synthase), NAAT (nicotianamine aminotransferase), and DMAS (deoxymugineic acid synthase). Many transporters required for Fe uptake from the rhizosphere and internal translocation have also been identified in rice. In addition, the signaling networks composed of various transcription factors (such as IDEF1, IDEF2, and members of the bHLH (basic helix-loop-helix) family), phytohormones, and signaling molecules are demonstrated to regulate Fe uptake and translocation. This knowledge greatly contributes to our understanding of the molecular mechanisms underlying iron deficiency responses in rice.

The Combined Strategy for iron uptake is not exclusive to domesticated rice (Oryza sativa)

Iron (Fe) is an essential micronutrient that is frequently inaccessible to plants. Rice (Oryza sativa L.) plants employ the Combined Strategy for Fe uptake, which is composed by all features of Strategy II, common to all Poaceae species, and some features of Strategy I, common to non-Poaceae species. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe deficiency in O. sativa and its wild progenitor O. rufipogon. We identified 622 and 2,017 differentially expressed genes in O. sativa and O. rufipogon, respectively. Among the genes up-regulated in both species, we found Fe transporters associated with Strategy I, such as IRT1, IRT2 and NRAMP1; and genes associated with Strategy II, such as YSL15 and IRO2. In order to evaluate the conservation of these Strategies among other Poaceae, we identified the orthologs of these genes in nine species from the Oryza genus, maize and sorghum, and evaluated their expression profile in response to low Fe condition. Our results indicate that the Combined Strategy is not specific to O. sativa as previously proposed, but also present in species of the Oryza genus closely related to domesticated rice, and originated around the same time the AA genome lineage within Oryza diversified. Therefore, adaptation to Fe2+ acquisition via IRT1 in flooded soils precedes O. sativa domestication.

Dissecting molecular mechanisms underlying salt tolerance in rice: a comparative transcriptional profiling of the contrasting genotypes

BACKGROUND

Salinity expansion in arable land is a threat to crop plants. Rice is the staple food crop across several countries worldwide; however, its salt sensitive nature severely affects its growth under excessive salinity. FL478 is a salt tolerant indica recombinant inbred line, which can be a good source of salt tolerance at the seedling stage in rice. To learn about the genetic basis of its tolerance to salinity, we compared transcriptome profiles of FL478 and its sensitive parent (IR29) using RNA-seq technique.

RESULTS

A total of 1714 and 2670 genes were found differentially expressed (DEGs) under salt stress compared to normal conditions in FL478 and IR29, respectively. Gene ontology analysis revealed the enrichment of transcripts involved in salinity response, regulation of gene expression, and transport in both genotypes. Comparative transcriptome analysis revealed that 1063 DEGs were co-expressed, while 338/252 and 572/908 DEGs were exclusively up/down-regulated in FL478 and IR29, respectively. Further, some biological processes (e.g. iron ion transport, response to abiotic stimulus, and oxidative stress) and molecular function terms (e.g. zinc ion binding and cation transmembrane transporter activity) were specifically enriched in FL478 up-regulated transcripts. Based on the metabolic pathways analysis, genes encoding transport and major intrinsic proteins transporter superfamily comprising aquaporin subfamilies and genes involved in MAPK signaling and signaling receptor kinases were specifically enriched in FL478. A total of 1135 and 1894 alternative splicing events were identified in transcripts of FL478 and IR29, respectively. Transcripts encoding two potassium transporters and two major facilitator family transporters were specifically up-regulated in FL478 under salt stress but not in the salt sensitive genotype. Remarkably, 11 DEGs were conversely regulated in the studied genotypes; for example, OsZIFL, OsNAAT, OsGDSL, and OsELIP genes were up-regulated in FL478, while they were down-regulated in IR29.

CONCLUSIONS

The achieved results suggest that FL478 employs more efficient mechanisms (especially in signal transduction of salt stress, influx and transport of k⁺, ionic and osmotic homeostasis, as well as ROS inhibition) to respond to the salt stress compared to its susceptible parent.

Tolerance of Iron-Deficient and -Toxic Soil Conditions in Rice

Iron (Fe) deficiency and toxicity are the most widely prevalent soil-related micronutrient disorders in rice (Oryza sativa L.). Progress in rice cultivars with improved tolerance has been hampered by a poor understanding of Fe availability in the soil, the transportation mechanism, and associated genetic factors for the tolerance of Fe toxicity soil (FTS) or Fe deficiency soil (FDS) conditions. In the past, through conventional breeding approaches, rice varieties were developed especially suitable for low- and high-pH soils, which indirectly helped the varieties to tolerate FTS and FDS conditions. Rice-Fe interactions in the external environment of soil, internal homeostasis, and transportation have been studied extensively in the past few decades. However, the molecular and physiological mechanisms of Fe uptake and transport need to be characterized in response to the tolerance of morpho-physiological traits under Fe-toxic and -deficient soil conditions, and these traits need to be well integrated into breeding programs. A deeper understanding of the several factors that influence Fe absorption, uptake, and transport from soil to root and above-ground organs under FDS and FTS is needed to develop tolerant rice cultivars with improved grain yield. Therefore, the objective of this review paper is to congregate the different phenotypic screening methodologies for prospecting tolerant rice varieties and their responsible genetic traits, and Fe homeostasis related to all the known quantitative trait loci (QTLs), genes, and transporters, which could offer enormous information to rice breeders and biotechnologists to develop rice cultivars tolerant of Fe toxicity or deficiency. The mechanism of Fe regulation and transport from soil to grain needs to be understood in a systematic manner along with the cascade of metabolomics steps that are involved in the development of rice varieties tolerant of FTS and FDS. Therefore, the integration of breeding with advanced genome sequencing and omics technologies allows for the fine-tuning of tolerant genotypes on the basis of molecular genetics, and the further identification of novel genes and transporters that are related to Fe regulation from FTS and FDS conditions is incredibly important to achieve further success in this aspect.

OsYSL13 Is Involved in Iron Distribution in Rice

The uptake and transport of iron (Fe) in plants are both important for plant growth and human health. However, little is known about the mechanism of Fe transport in plants, especially for crops. In the present study, the function of yellow stripe-like 13 (YSL13) in rice was analyzed. OsYSL13 was highly expressed in leaves, especially in leaf blades, whereas its expression was induced by Fe deficiency both in roots and shoots. Furthermore, the expression level of OsYSL13 was higher in older leaves than that in younger leaves. OsYSL13 was located in the plasma membrane. Metal measurement revealed that Fe concentrations were lower in the youngest leaf and higher in the older leaves of the osysl13 mutant under both Fe sufficiency and deficiency conditions, compared with the wild type and two complementation lines. Moreover, the Fe concentrations in the brown rice and seeds of the osysl13 mutant were also reduced. Opposite results were found in OsYSL13 overexpression lines. These results suggest that OsYSL13 is involved in Fe distribution in rice.

Diurnal Changes in Transcript and Metabolite Levels during the Iron Deficiency Response of Rice

BACKGROUND

Rice (Oryza sativa L.) is highly susceptible to iron (Fe) deficiency due to low secretion levels of the mugineic acid (MA) family phytosiderophore (PS) 2'-deoxymugineic acid (DMA) into the rhizosphere. The low levels of DMA secreted by rice have proved challenging to measure and, therefore, the pattern of DMA secretion under Fe deficiency has been less extensively studied relative to other graminaceous monocot species that secrete high levels of PS, such as barley (Hordeum vulgare L.).

RESULTS

Gene expression and metabolite analyses were used to characterise diurnal changes occurring during the Fe deficiency response of rice. Iron deficiency inducible genes involved in root DMA biosynthesis and secretion followed a diurnal pattern with peak induction occurring 3-5 h after the onset of light; a result consistent with that of other Strategy II plant species such as barley and wheat. Furthermore, triple quadrupole mass spectrometry identified 3-5 h after the onset of light as peak time of DMA secretion from Fe-deficient rice roots. Metabolite profiling identified accumulation of amines associated with metal chelation, metal translocation and plant oxidative stress responses occurring with peak induction 10-12 h after the onset of light.

CONCLUSION

The results of this study confirmed that rice shares a similar peak time of Fe deficiency associated induction of DMA secretion compared to other Strategy II plant species but has less prominent daily fluctuations of DMA secretion. It also revealed metabolic changes associated with the remediation of Fe deficiency and mitigation of damage from resulting stress in rice roots. This study complements previous studies on the genetic changes in response to Fe deficiency in rice and constitutes an important advance towards our understanding of the molecular mechanisms underlying the rice Fe deficiency response.

The rice OsNAC6 transcription factor orchestrates multiple molecular mechanisms involving root structural adaptions and nicotianamine biosynthesis for drought tolerance

Drought has a serious impact on agriculture worldwide. A plant's ability to adapt to rhizosphere drought stress requires reprogramming of root growth and development. Although physiological studies have documented the root adaption for tolerance to the drought stress, underlying molecular mechanisms is still incomplete, which is essential for crop engineering. Here, we identified OsNAC6-mediated root structural adaptations, including increased root number and root diameter, which enhanced drought tolerance. Multiyear drought field tests demonstrated that the grain yield of OsNAC6 root-specific overexpressing transgenic rice lines was less affected by drought stress than were nontransgenic controls. Genome-wide analyses of loss- and gain-of-function mutants revealed that OsNAC6 up-regulates the expression of direct target genes involved in membrane modification, nicotianamine (NA) biosynthesis, glutathione relocation, 3'-phophoadenosine 5'-phosphosulphate accumulation and glycosylation, which represent multiple drought tolerance pathways. Moreover, overexpression of NICOTIANAMINE SYNTHASE genes, direct targets of OsNAC6, promoted the accumulation of the metal chelator NA and, consequently, drought tolerance. Collectively, OsNAC6 orchestrates novel molecular drought tolerance mechanisms and has potential for the biotechnological development of high-yielding crops under water-limiting conditions.

Dealing with iron metabolism in rice: from breeding for stress tolerance to biofortification

Iron is a well-known metal. Used by humankind since ancient times in many different ways, this element is present in all living organisms, where, unfortunately, it represents a two-way problem. Being an essential block in the composition of different proteins and metabolic pathways, iron is a vital component for animals and plants. That is why iron deficiency has a severe impact on the lives of different organisms, including humans, becoming a major concern, especially in developing countries where access to adequate nutrition is still difficult. On the other hand, this metal is also capable of causing damage when present in excess, becoming toxic to cells and affecting the whole organism. Because of its importance, iron absorption, transport and storage mechanisms have been extensively investigated in order to design alternatives that may solve this problem. As the understanding of the strategies that plants use to control iron homeostasis is an important step in the generation of improved plants that meet both human agricultural and nutritional needs, here we discuss some of the most important points about this topic.

Transcriptional and physiological analyses of Fe deficiency response in maize reveal the presence of Strategy I components and Fe/P interactions

Background

Under limited iron (Fe) availability maize, a Strategy II plant, improves Fe acquisition through the release of phytosiderophores (PS) into the rhizosphere and the subsequent uptake of Fe-PS complexes into root cells. Occurrence of Strategy-I-like components and interactions with phosphorous (P) nutrition has been hypothesized based on molecular and physiological studies in grasses.

Results

In this report transcriptomic analysis (NimbleGen microarray) of Fe deficiency response revealed that maize roots modulated the expression levels of 724 genes (508 up- and 216 down-regulated, respectively). As expected, roots of Fe-deficient maize plants overexpressed genes involved in the synthesis and release of 2’-deoxymugineic acid (the main PS released by maize roots). A strong modulation of genes involved in regulatory aspects, Fe translocation, root morphological modification, primary metabolic pathways and hormonal metabolism was induced by the nutritional stress. Genes encoding transporters for Fe²⁺ (ZmNRAMP1) and P (ZmPHT1;7 and ZmPHO1) were also up-regulated under Fe deficiency.

Fe-deficient maize plants accumulated higher amounts of P than the Fe-sufficient ones, both in roots and shoots. The supply of 1 μM ⁵⁹Fe, as soluble (Fe-Citrate and Fe-PS) or sparingly soluble (Ferrihydrite) sources to deficient plants, caused a rapid down-regulation of genes coding for PS and Fe(III)-PS transport, as well as of ZmNRAMP1 and ZmPHT1;7.

Levels of ³²P absorption essentially followed the rates of ⁵⁹Fe uptake in Fe-deficient plants during Fe resupply, suggesting that P accumulation might be regulated by Fe uptake in maize plants.

Conclusions

The transcriptional response to Fe-deficiency in maize roots confirmed the modulation of known genes involved in the Strategy II and revealed the presence of Strategy I components usually described in dicots. Moreover, data here presented provide evidence of a close relationship between two essential nutrients for plants, Fe and P, and highlight a key role played by Fe and P transporters to preserve the homeostasis of these two nutrients in maize plants.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3478-4) contains supplementary material, which is available to authorized users.

Molybdenum and iron mutually impact their homeostasis in cucumber (Cucumis sativus) plants

Molybdenum (Mo) and iron (Fe) are essential micronutrients required for crucial enzyme activities in plant metabolism. Here we investigated the existence of a mutual control of Mo and Fe homeostasis in cucumber (Cucumis sativus). Plants were grown under single or combined Mo and Fe starvation. Physiological parameters were measured, the ionomes of tissues and the ionomes and proteomes of root mitochondria were profiled, and the activities of molybdo-enzymes and the synthesis of molybdenum cofactor (Moco) were evaluated. Fe and Mo were found to affect each other's total uptake and distribution within tissues and at the mitochondrial level, with Fe nutritional status dominating over Mo homeostasis and affecting Mo availability for molybdo-enzymes in the form of Moco. Fe starvation triggered Moco biosynthesis and affected the molybdo-enzymes, with its main impact on nitrate reductase and xanthine dehydrogenase, both being involved in nitrogen assimilation and mobilization, and on the mitochondrial amidoxime reducing component. These results, together with the identification of > 100 proteins differentially expressed in root mitochondria, highlight the central role of mitochondria in the coordination of Fe and Mo homeostasis and allow us to propose the first model of the molecular interactions connecting Mo and Fe homeostasis.

Efficient acquisition of iron confers greater tolerance to saline-alkaline stress in rice (Oryza sativa L.)

To elucidate the mechanisms underlying tolerance to saline-alkaline stress in two rice genotypes, Dongdao-4 and Jigeng-88, we exposed them to medium supplemented with 10 mM Na2CO3 and 40 mM NaCl (pH 8.5). Dongdao-4 plants displayed higher biomass, chlorophyll content, and photosynthetic rates, and a larger root system than Jigeng-88 under saline-alkaline conditions. Dongdao-4 had a higher shoot Na+/K+ ratio than Jigeng-88 under both control and saline-alkaline conditions. Dongdao-4 exhibited stronger rhizospheric acidification than Jigeng-88 under saline-alkaline conditions, resulting from greater up-regulation of H+-ATPases at the transcriptional level. Moreover, Fe concentrations in shoots and roots of Dongdao-4 were higher than those in Jigeng-88, and a higher rate of phytosiderophore exudation was detected in Dongdao-4 versus Jigeng-88 under saline-alkaline conditions. The Fe-deficiency-responsive genes OsIRO2, OsIRT1, OsNAS1, OsNAS2, OsYSL2, and OsYSL15 were more strongly up-regulated in Dongdao-4 than Jigeng-88 plants in saline-alkaline medium, implying greater tolerance of Dongdao-4 plants to Fe deficiency. To test this hypothesis, we compared the effects of Fe deficiency on the two genotypes, and found that Dongdao-4 was more tolerant to Fe deficiency. Exposure to Fe-deficient medium led to greater rhizospheric acidification and phytosiderophore exudation in Dongdao-4 than Jigeng-88 plants. Expression levels of OsIRO2, OsIRT1, OsNAS1, OsNAS2, OsYSL2, and OsYSL15 were higher in Dongdao-4 than Jigeng-88 plants under Fe-deficient conditions. These results demonstrate that a highly efficient Fe acquisition system together with a large root system may underpin the greater tolerance of Dongdao-4 plants to saline-alkaline stress.

Jasmonate signaling is activated in the very early stages of iron deficiency responses in rice roots

Under low iron availability, plants induce the expression of various genes involved in iron uptake and translocation at the transcriptional level. This iron deficiency response is affected by various plant hormones, but the roles of jasmonates in this response are not well-known. We investigated the involvement of jasmonates in rice iron deficiency responses. High rates of jasmonate-inducible genes were induced during the very early stages of iron deficiency treatment in rice roots. Many jasmonate-inducible genes were also negatively regulated by the ubiquitin ligases OsHRZ1 and OsHRZ2 and positively regulated by the transcription factor IDEF1. Ten out of 35 genes involved in jasmonate biosynthesis and signaling were rapidly induced at 3 h of iron deficiency treatment, and this induction preceded that of known iron deficiency-inducible genes involved in iron uptake and translocation. Twelve genes involved in jasmonate biosynthesis and signaling were also upregulated in HRZ-knockdown roots. Endogenous concentrations of jasmonic acid and jasmonoyl isoleucine tended to be rapidly increased in roots in response to iron deficiency treatment, whereas these concentrations were higher in HRZ-knockdown roots under iron-sufficient conditions. Analysis of the jasmonate-deficient cpm2 mutant revealed that jasmonates repress the expression of many iron deficiency-inducible genes involved in iron uptake and translocation under iron sufficiency, but this repression is partly canceled under an early stage of iron deficiency. These results indicate that jasmonate signaling is activated during the very early stages of iron deficiency, which is partly regulated by IDEF1 and OsHRZs.

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.

Living to Die and Dying to Live: The Survival Strategy behind Leaf Senescence

Senescence represents the final developmental act of the leaf, during which the leaf cell is dismantled in a coordinated manner to remobilize nutrients and to secure reproductive success. The process of senescence provides the plant with phenotypic plasticity to help it adapt to adverse environmental conditions. Here, we provide a comprehensive overview of the factors and mechanisms that control the onset of senescence. We explain how the competence to senesce is established during leaf development, as depicted by the senescence window model. We also discuss the mechanisms by which phytohormones and environmental stresses control senescence as well as the impact of source-sink relationships on plant yield and stress tolerance. In addition, we discuss the role of senescence as a strategy for stress adaptation and how crop production and food quality could benefit from engineering or breeding crops with altered onset of senescence.

Co-operative intermolecular kinetics of 2-oxoglutarate dependent dioxygenases may be essential for system-level regulation of plant cell physiology

Can the stimulus-driven synergistic association of 2-oxoglutarate dependent dioxygenases be influenced by the kinetic parameters of binding and catalysis?In this manuscript, I posit that these indices are necessary and specific for a particular stimulus, and are key determinants of a dynamic clustering that may function to mitigate the effects of this trigger. The protein(s)/sequence(s) that comprise this group are representative of all major kingdoms of life, and catalyze a generic hydroxylation, which is, in most cases accompanied by a specialized conversion of the substrate molecule. Iron is an essential co-factor for this transformation and the response to waning levels is systemic, and mandates the simultaneous participation of molecular sensors, transporters, and signal transducers. Here, I present a proof-of-concept model, that an evolving molecular network of 2OG-dependent enzymes can maintain iron homeostasis in the cytosol of root hair cells of members of the family Gramineae by actuating a non-reductive compensatory chelation by the phytosiderophores. Regression models of empirically available kinetic data (iron and alpha-ketoglutarate) were formulated, analyzed, and compared. The results, when viewed in context of the superfamily responding as a unit, suggest that members can indeed, work together to accomplish system-level function. This is achieved by the establishment of transient metabolic conduits, wherein the flux is dictated by kinetic compatibility of the participating enzymes. The approach adopted, i.e., predictive mathematical modeling, is integral to the hypothesis-driven acquisition of experimental data points and, in association with suitable visualization aids may be utilized for exploring complex plant biochemical systems.

Transcriptomic analysis of rice in response to iron deficiency and excess

BACKGROUND

Iron (Fe) is essential micronutrient for plants and its deficiency as well as toxicity is a serious agricultural problem. The mechanisms of Fe deficiency are reasonably understood, however our knowledge about plants response to excess Fe is limited. Moreover, the regulation of small open reading frames (sORFs) in response to abiotic stress has not been reported in rice. Understanding the regulation of rice transcriptome in response to Fe deficiency and excess could provide bases for developing strategies to breed plants tolerant to Fe deficiency as well as excess Fe.

RESULTS

We used a novel rice 110 K microarray harbouring ~48,620 sORFs to understand the transcriptomic changes that occur in response to Fe deficiency and excess. In roots, 36 genes were upregulated by excess Fe, of which three were sORFs. In contrast, 1509 genes were upregulated by Fe deficiency, of which 90 (6%) were sORFs. Co-expression analysis revealed that the expression of some sORFs was positively correlated with the genes upregulated by Fe deficiency. In shoots, 50 (19%) of the genes upregulated by Fe deficiency and 1076 out of 2480 (43%) genes upregulated by excess Fe were sORFs. These results suggest that excess Fe may significantly alter metabolism, particularly in shoots.

CONCLUSION

These data not only reveal the genes regulated by excess Fe, but also suggest that sORFs might play an important role in the response of plants to Fe deficiency and excess.

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.

Membrane transporters mediating root signalling and adaptive responses to oxygen deprivation and soil flooding

This review provides a comprehensive assessment of a previously unexplored topic: elucidating the role that plasma- and organelle-based membrane transporters play in plant-adaptive responses to flooding. We show that energy availability and metabolic shifts under hypoxia and anoxia are critical in regulating membrane-transport activity. We illustrate the high tissue and time dependence of this regulation, reveal the molecular identity of transporters involved and discuss the modes of their regulation. We show that both reduced oxygen availability and accumulation of transition metals in flooded roots result in a reduction in the cytosolic K(+) pool, ultimately determining the cell's fate and transition to programmed cell death (PCD). This process can be strongly affected by hypoxia-induced changes in the amino acid pool profile and, specifically, ϒ-amino butyric acid (GABA) accumulation. It is suggested that GABA plays an important regulatory role, allowing plants to proceed with H2 O2 signalling to activate a cascade of genes that mediate plant adaptation to flooding while at the same time, preventing the cell from entering a 'suicide program'. We conclude that progress in crop breeding for flooding tolerance can only be achieved by pyramiding the numerous physiological traits that confer efficient energy maintenance, cytosolic ion homeostasis, and reactive oxygen species (ROS) control and detoxification.

Tissue-specific transcriptional profiling of iron-deficient and cadmium-stressed rice using laser capture microdissection

Several metals are essential nutrients for plants. However, they become toxic at high levels and deleteriously affect crop yield and quality. We recently reported the spatial gene expression profiles of iron (Fe)-deficient and cadmium (Cd)-stressed rice using laser microdissection and microarray analysis. The roots of Fe-deficient and Cd-stressed rice were separated into the vascular bundle (VB), cortex (Cor), and epidermis plus exodermis (EP). In addition, vascular bundles from new and old leaves at the lowest node, which are important for metal distribution, were analyzed separately (newDC and oldDC, respectively). Genes expressed in a tissue-specific manner in the VB, Cor, EP, newDC, and oldDC formed large clusters. The genes upregulated in all of the VB, Cor, and EP by Fe deficiency formed a substantial cluster that was smaller than the tissue-specific clusters. Significant numbers of genes expressed in newDC or oldDC were also expressed in VB in roots, suggesting that vascular bundles in the lowest nodes and roots have a partially common function. The expression patterns of transporter families involved in metal homeostasis were investigated, and members of each family were either expressed differentially in each tissue or showed different responses to Fe deficiency. One potassium transporter gene, OsHAK22, was upregulated by Fe deficiency in VB, Cor, and EP, suggesting that OsHAK22 is involved in potassium transport associated with mugineic acids secretion.