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Declines in crop productivity that are thought to be due to iron deficiency have been reported even on non-calcareous-alkaline soils. For example, tomatoes exhibit iron deficiency-like symptoms (yellowing of new leaves) if the fruit load is heavy during winter. The objective of this study is to investigate the relationship between fruit load, low temperatures, low sunlight, and iron deficiency, and to explore the possibility of increasing productivity with iron-containing fertilizers. Results of an investigation of the farms experiencing iron deficiency-like symptoms in winter showed low iron concentrations and elevated expression of iron deficiency-inducible genes in yellowing leaves. To investigate the effects of heavy fruit load on iron nutrition, plants were grown in three groups: those with a medium number of fruits per truss (MED), a high number of fruits (heavy fruit load; HEAVY), and a high number of fruits with additional iron fertilization (++Fe). The SPAD leaf-color value of the new leaves and weight of the lower leaves in winter were in the order of HEAVY < ++Fe < MED. In all groups, the iron concentrations in the upper leaves in January were lower than those in October and March. RNA-seq analysis showed that the expression of genes involved in iron absorption was suppressed in the roots in January, which may have contributed to iron deficiency in winter. These results suggest that one of the factors limiting the productivity of tomatoes in winter with heavy fruit load is iron, and that productivity can be restored by iron materials. [ABSTRACT FROM AUTHOR]

Iron is essential for most living organisms and is required for normal plant growth. Plants induce iron utilization systems under conditions of low iron availability, but the molecular mechanisms of this gene regulation system remain largely unknown. We identified the rice transcription factor IDEF1, which specifically binds the iron-deficiency-responsive cis-acting element IDE1. IDEF1 belongs to an uncharacterized branch of the plant-specific transcription factor family ABI3/VP1 and efficiently binds to the CATGC sequence within IDE1. IDEF1 transcripts are constitutively present in rice roots and leaves. Transgenic tobacco plants expressing IDEF1 under the control of the constitutive cauliflower mosaic virus 35S promoter transactivate IDE1-mediated expression only in iron-deficient roots. Transgenic rice plants expressing IDEF1 under the control of the iron-deficiency-inducible IDS2 promoter tolerate iron deficiency in hydroponic culture and calcareous soil. Conversely, transgenic rice plants with repressed IDEF1 expression are susceptible to early stage iron deficiency in hydroponic culture. Expression analysis of these transgenic plants revealed that IDEF1 positively regulates iron-deficiency-induced genes, including the ferrous iron transporter gene OsIRT1 and the iron-deficiency-induced transcription factor gene OsIRO2. These data suggest the presence of a sequential gene regulatory network that functions via novel cis element/trans factor interactions to promote the iron-deficiency response.

Iron deficiency is a worldwide agricultural problem on calcareous soils with low iron (Fe) availability and also poses a major human nutritional problem. Plants induce Fe-acquisition systems under conditions of low Fe availability. Previously, we reported that an Fe deficiency-inducible bHLH transcription factor, OsIRO2, is responsible for regulating the genes involved in Fe homeostasis in rice. Here, we show that OsIRO2 overexpression results in improved tolerance to low Fe availability in calcareous soil. In addition to increased Fe content in shoots, rice overexpressing OsIRO2 accumulates more Fe in seeds than non-transformant rice when grown on calcareous soil. OsIRO2 promoter–GUS analysis revealed that OsIRO2 expression could be detected in developing seeds. These results suggest that OsIRO2 plays a crucial role in regulating both Fe uptake from soil and Fe translocation to grain. Improved uptake and translocation of Fe in the OsIRO2-overexpressing rice under low Fe availability provides an approach for producing graminaceous crops that are tolerant to Fe deficiency and have Fe-rich seeds to enhance production and the nutritional quality of food.

Iron (Fe) is essential for most living organisms, and thus Fe deficiency poses a major abiotic stress in crop production. Plants induce Fe utilization systems under conditions of low-Fe availability, but the molecular mechanisms of gene regulation under Fe deficiency remain largely unknown. We identified a novel transcription factor in rice and barley, IDEF2, which specifically binds to the Fe deficiency-responsive cis-acting element 2 (IDE2), using yeast one-hybrid screening. IDEF2 belongs to an uncharacterized branch of the NAC transcription factor family and exhibits novel properties of sequence recognition. An electrophoretic mobility shift assay and cyclic amplification and selection of targets (CASTing) experiment revealed that IDEF2 predominantly recognizes CA[A/C]G[T/C][T/C/A][T/C/A] within IDE2 as the core binding site. IDEF2 transcripts are constitutively present in rice roots and leaves. Repression of the function of IDEF2 by RNA interference (RNAi) and chimeric repressor gene-silencing technology (CRES-T) caused aberrant Fe distribution between shoots and roots in rice grown hydroponically under Fe-sufficient or deficient conditions. These results reveal novel cis-element/trans-factor interactions that are functionally associated with iron homeostasis.

Iron (Fe) is critical for plant growth. Under conditions of low Fe availability, rice plants induce genes involved in Fe uptake and utilization. Recently, we identified the iron-deficiency-responsive cis-acting elements IDE1 and IDE2, which are bound in a specific manner by IDE-binding factors 1 and 2 (IDEF1 and IDEF2, respectively). IDEF1 and IDEF2 regulate genes related to the Fe-deficiency response. In the present study, we examined the spatial expression patterns of IDEF1 and IDEF2 during the germination, vegetative, and seed-maturation stages by assessing their localization in IDEF1 and IDEF2 promoter–GUS transgenic rice lines. During germination, IDEF1 and IDEF2 were expressed in the endosperm and embryo. In hydroponic culture experiments, the expression patterns of IDEF1 and IDEF2 were similar under both Fe-deficient and Fe-sufficient conditions during the vegetative stage. In leaves, IDEF1 expression was observed in mesophyll cells and in small vascular bundles, whereas IDEF2 was highly expressed in vascular bundles. In root sections, IDEF1 and IDEF2 were highly expressed in secondary roots and inside vascular bundles. IDEF1 was also expressed in pollen from flowers before and after anthesis, in the ovary after fertilization, and in the embryo during seed maturation. IDEF2 was expressed in flowering stage pollen, in immature seeds just after flowering, and in the dorsal vascular region during the late maturation stage. The spatial expression patterns of IDEF1 and IDEF2 partially overlapped with their target genes.

Although the genes involved in metal homeostasis have been investigated over the past few decades, many genes related to metal homeostasis remain uncharacterized, and a comprehensive analysis of the expression of these genes is required., In the present study, we investigated the spatial gene expression profile of iron (Fe)-deficient and cadmium (Cd)-stressed Oryza sativa (rice) using laser microdissection and microarray analysis. Roots of Fe-deficient and Cd-stressed rice were separated into the vascular bundle, cortex, and epidermis plus exodermis. In addition, vascular bundles from new and old leaves at the lowest node, which are important for metal distribution, were analyzed separately., The spatial expression patterns were distinct in each tissue type. Fe deficiency and Cd stress also had significant effects on the transcriptomes, although these were less pronounced than the spatial effects. Genes encoding transporters involved in metal homeostasis, proteins associated with heavy metal detoxification, and phytohormone-related proteins were comprehensively investigated. Additionally, cis motifs involved in the regulation of these diverse expression changes in various tissue types were predicted., The spatial transcriptomes presented here provide novel insight into the molecular mechanisms of metal homeostasis. [ABSTRACT FROM AUTHOR]

Background: Cis-acting elements are essential genomic sequences that control gene expression. In higher eukaryotes, a series of cis-elements function cooperatively. However, further studies are required to examine the co-regulation of multiple cis-elements on a promoter. The aim of this study was to propose a model of cis-element networks that cooperatively regulate gene expression in rice under iron (Fe) deficiency. Results: We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. Based on sequences of Oryza sativa genes upregulated by Fe deficiency, MAMA returned experimentally identified cis-elements responsible for Fe deficiency in O. sativa. When this method was applied to O. sativa subjected to zinc deficiency and Arabidopsis thaliana subjected to salt stress, several novel candidate cis-acting elements that overlap with known cis-acting elements, such as ZDRE, ABRE, and DRE, were identified. After optimization, MAMA accurately simulated more than 87% of gene expression. Predicted motifs strongly co-localized in the upstream regions of regulated genes and sequences around transcription start sites. Furthermore, in many cases, the separation (in bp) between co-localized motifs was conserved, suggesting that predicted motifs and the separation between them were important in the co-regulation of gene expression. Conclusions: Our results are suggestive of a typical sequence model for Fe deficiency-responsive promoters and some strong candidate cis-elements that function cooperatively with known cis-elements. [ABSTRACT FROM AUTHOR]