Involvement of the ABCG37 transporter in secretion of scopoletin and derivatives by Arabidopsis roots in response to iron deficiency

Specialized metabolite modifications in Brassicaceae seeds and plants: diversity, functions and related enzymes

Covering: up to 2023Specialized metabolite (SM) modifications and/or decorations, corresponding to the addition or removal of functional groups (e.g. hydroxyl, methyl, glycosyl or acyl group) to SM structures, contribute to the huge diversity of structures, activities and functions of seed and plant SMs. This review summarizes available knowledge (up to 2023) on SM modifications in Brassicaceae and their contribution to SM plasticity. We give a comprehensive overview on enzymes involved in the addition or removal of these functional groups. Brassicaceae, including model (Arabidopsis thaliana) and crop (Brassica napus, Camelina sativa) plant species, present a large diversity of plant and seed SMs, which makes them valuable models to study SM modifications. In this review, particular attention is given to the environmental plasticity of SM and relative modification and/or decoration enzymes. Furthermore, a spotlight is given to SMs and related modification enzymes in seeds of Brassicaceae species. Seeds constitute a large reservoir of beneficial SMs and are one of the most important dietary sources, providing more than half of the world's intake of dietary proteins, oil and starch. The seed tissue- and stage-specific expressions of A. thaliana genes involved in SM modification are presented and discussed in the context of available literature. Given the major role in plant phytochemistry, biology and ecology, SM modifications constitute a subject of study contributing to the research and development in agroecology, pharmaceutical, cosmetics and food industrial sectors.

bHLH121 and clade IVc bHLH transcription factors synergistically function to regulate iron homeostasis in Arabidopsis thaliana

Iron is an essential micronutrient for plant growth and development. In Arabidopsis thaliana, an intricate regulatory network involving several basic helix-loop-helix (bHLH) transcription factors controls the homeostasis of iron. Among these transcription factors, bHLH121 plays a crucial role. bHLH121 interacts in vivo with clade IVc bHLH transcription factors and activates the expression of FIT and clade Ib bHLH transcription factors to stimulate the uptake of iron. How bHLH121 and clade IVc bHLH transcription factors function collectively and efficiently to maintain iron homeostasis is still unclear. Herein, we found that double loss-of-function mutants involving bhlh121 and one of the clade IVc bHLH transcription factors displayed more severe iron deficiency-associated growth defects than each of the single mutants. We also found that among the four clade IVc bHLH transcription factors, only bHLH34 and bHLH105 could partially complement the iron-associated growth defects of bhlh121 when overexpressed. These data, together with protein localization analysis, support that bHLH121 and clade IVc bHLH transcription factors act synergistically to regulate iron homeostasis and that different bHLH121/clade IVc and clade IVc/clade IVc protein complexes are involved in this process.

Two diversities meet in the rhizosphere: root specialized metabolites and microbiome

Plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes, including interactions with various microbes both beneficial and harmful. Considering microbes as bioreactors, the chemical diversity undergoes dynamic changes when root-derived specialized metabolites (RSMs) and microbes encounter each other in the rhizosphere. Recent advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe interactions. In this review, we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health, incorporating the most up-to-date information available. Additionally, we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the environment. Finally, we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.

Biosynthesis of Scopoletin in Sweet Potato Confers Resistance against Fusarium oxysporum

Fusarium wilt is a severe fungal disease caused by Fusarium oxysporum in sweet potato. We conducted transcriptome analysis to explore the resistance mechanism of sweet potato against F. oxysporum. Our findings highlighted the role of scopoletin, a hydroxycoumarin, in enhancing resistance. In vitro experiments confirmed that scopoletin and umbelliferone had inhibitory effects on the F. oxysporum growth. We identified hydroxycoumarin synthase genes IbF6'H2 and IbCOSY that are responsible for scopoletin production in sweet potatoes. The co-overexpression of IbF6'H2 and IbCOSY in tobacco plants produced the highest scopoletin levels and disease resistance. This study provides insights into the molecular basis of sweet potato defense against Fusarium wilt and identifies valuable genes for breeding wilt-resistant cultivars.

Molecular insights into the mutualism that induces iron deficiency tolerance in sorghum inoculated with Trichoderma harzianum

Iron (Fe) deficiency is a common mineral stress in plants, including sorghum. Although the soil fungus Trichoderma harzianum has been shown to mitigate Fe deficiency in some circumstances, neither the range nor mechanism(s) of this process are well understood. In this study, high pH-induced Fe deficiency in sorghum cultivated in pots with natural field soil exhibited a significant decrease in biomass, photosynthetic rate, transpiration rate, stomatal conductance, water use efficiency, and Fe-uptake in both the root and shoot. However, the establishment of T. harzianum colonization in roots of Fe-deprived sorghum showed significant improvements in morpho-physiological traits, Fe levels, and redox status. Molecular detection of the fungal ThAOX1 (L-aminoacid oxidase) gene showed the highest colonization of T. harzianum in the root tips of Fe-deficient sorghum, a location thus targeted for further analysis. Expression studies by RNA-seq and qPCR in sorghum root tips revealed a significant upregulation of several genes associated with Fe uptake (SbTOM2), auxin synthesis (SbSAURX15), nicotianamine synthase 3 (SbNAS3), and a phytosiderophore transporter (SbYS1). Also induced was the siderophore synthesis gene (ThSIT1) in T. harzianum, a result supported by biochemical evidence for elevated siderophore and IAA (indole acetic acid) levels in roots. Given the high affinity of fungal siderophore to chelate insoluble Fe3+ ions, it is likely that elevated siderophore released by T. harzianum led to Fe(III)-siderophore complexes in the rhizosphere that were then transported into roots by the induced SbYS1 (yellow-stripe 1) transporter. In addition, the observed induction of several plant peroxidase genes and ABA (abscisic acid) under Fe deficiency after inoculation with T. harzianum may have helped induce tolerance to Fe-deficiency-induced oxidative stress and adaptive responses. This is the first mechanistic explanation for T. harzianum's role in helping alleviate Fe deficiency in sorghum and suggests that biofertilizers using T. harzianum will improve Fe availability to crops in high pH environments.

PDR9 allelic variation and MYB63 modulate nutrient-dependent coumarin homeostasis in Arabidopsis

Plant roots release phytochemicals into the soil environment to influence nutrient availability and uptake. Arabidopsis thaliana roots release phenylpropanoid coumarins in response to iron (Fe) deficiency, likely to enhance Fe uptake and improve plant health. This response requires sufficient phosphorus (P) in the root environment. Nonetheless, the regulatory interplay influencing coumarin production under varying availabilities of Fe and P is not known. Through genome-wide association studies, we have pinpointed the influence of the ABC transporter G family member, PDR9, on coumarin accumulation and trafficking (homeostasis) under combined Fe and P deficiency. We show that genetic variation in the promoter of PDR9 regulates its expression in a manner associated with coumarin production. Furthermore, we find that MYB63 transcription factor controls dedicated coumarin production by regulating both COUMARIN SYNTHASE (COSY) and FERULOYL-CoA 6'-HYDROXYLASE 1 (F6'H1) expression while orchestrating secretion through PDR9 genes under Fe and P combined deficiency. This integrated approach illuminates the intricate connections between nutrient signaling pathways in coumarin response mechanisms.

A major role of coumarin-dependent ferric iron reduction in strategy I-type iron acquisition in Arabidopsis

Many non-graminaceous species release various coumarins in response to iron (Fe) deficiency. However, the physiological relevance of these coumarins remains poorly understood. Here, we show that the three enzymes leading to sideretin biosynthesis co-exist in Arabidopsis (Arabidopsis thaliana) epidermal and cortical cells and that the shift to fraxetin at alkaline pH depends on MYB72-mediated repression of CYTOCHROME P450, FAMILY 82, SUBFAMILY C, POLYPEPTIDE 4 (CYP82C4). In vitro, only fraxetin and sideretin can reduce part of the Fe(III) that they mobilize. We demonstrate that coumarin-mediated Fe(III) reduction is critical under acidic conditions, as fraxetin and sideretin can complement the Fe(III)-chelate reductase mutant ferric reduction oxidase 2 (fro2), and disruption of coumarin biosynthesis in fro2 plants impairs Fe acquisition similar to in the Fe(II) uptake-deficient mutant iron-regulated transporter 1 (irt1). Disruption of sideretin biosynthesis in a fro2 cyp82C4-1 double mutant revealed that sideretin is the dominant chemical reductant that functions with FRO2 to mediate Fe(II) formation for root uptake. At alkaline pH, Fe(III) reduction by coumarins becomes almost negligible but fraxetin still sustains high Fe(III) mobilization, suggesting that its main function is to provide chelated Fe(III) for FRO2. Our study indicates that strategy-I plants link sideretin and fraxetin biosynthesis and secretion to external pH to recruit distinct coumarin chemical activities to maximize Fe acquisition according to prevailing soil pH conditions.

Enhanced phenylpropanoid metabolism underlies resistance to Fusarium oxysporum f. sp. vasinfectum race 4 infection in the cotton cultivar Pima-S6 (Gossypium barbadense L.)

Introduction: Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4) is a highly pathogenic soil-borne fungus responsible for Fusarium wilt in cotton (Gossypium spp.) and represents a continuing threat to cotton production in the southwest states of the United States, including California, New Mexico, and Texas. Pima (G. barbadense L.) cotton, which is highly valued for its fiber quality, has been shown to be more susceptible to this pathogen than Upland (G. hirsutum L.) cotton. Still, some Pima cultivars present resistance to FOV4 infection. Methods: To gain insights into the FOV4-resistance mechanism, we performed comparative transcriptional and metabolomic analyses between FOV4-susceptible and FOV4-resistant Pima cotton entries. FOV4-resistant Pima-S6 and FOV4-susceptible Pima S-7 and Pima 3-79 cotton plants were infected with FOV4 in the greenhouse, and the roots harvested 11 days post-infection for further analysis. Results: We found that an enhanced root phenylpropanoid metabolism in the resistant Pima-S6 cultivar determines FOV4-resistance. Gene-ontology enrichment of phenylpropanoid biosynthesis and metabolism categories correlated with the accumulation of secondary metabolites in Pima-S6 roots. Specifically, we found esculetin, a coumarin, an inhibitor of Fusarium's growth, accumulated in the roots of Pima-S6 even under non-infected conditions. Genes related to the phenylpropanoid biosynthesis and metabolism, including phenylalanine ammonia-lyase 2 (PAL2) and pleiotropic drug resistance 12 (PDR12) transporter, were found to be upregulated in Pima-S6 roots. Discussion: Our results highlight an essential role for the phenylpropanoid synthesis pathway in FOV4 resistance in Pima-S6 cotton. These genes represent attractive research prospects for FOV4-disease resistance and breeding approaches of other cotton cultivars of economic relevance.

GmABCG5, an ATP-binding cassette G transporter gene, is involved in the iron deficiency response in soybean

Iron deficiency is a major nutritional problem causing iron deficiency chlorosis (IDC) and yield reduction in soybean, one of the most important crops. The ATP-binding cassette G subfamily plays a crucial role in substance transportation in plants. In this study, we cloned the GmABCG5 gene from soybean and verified its role in Fe homeostasis. Analysis showed that GmABCG5 belongs to the ABCG subfamily and is subcellularly localized at the cell membrane. From high to low, GmABCG5 expression was found in the stem, root, and leaf of young soybean seedlings, and the order of expression was flower, pod, seed stem, root, and leaf in mature soybean plants. The GUS assay and qRT-PCR results showed that the GmABCG5 expression was significantly induced by iron deficiency in the leaf. We obtained the GmABCG5 overexpressed and inhibitory expressed soybean hairy root complexes. Overexpression of GmABCG5 promoted, and inhibition of GmABCG5 retarded the growth of soybean hairy roots, independent of nutrient iron conditions, confirming the growth-promotion function of GmABCG5. Iron deficiency has a negative effect on the growth of soybean complexes, which was more obvious in the GmABCG5 inhibition complexes. The chlorophyll content was increased in the GmABCG5 overexpression complexes and decreased in the GmABCG5 inhibition complexes. Iron deficiency treatment widened the gap in the chlorophyll contents. FCR activity was induced by iron deficiency and showed an extraordinary increase in the GmABCG5 overexpression complexes, accompanied by the greatest Fe accumulation. Antioxidant capacity was enhanced when GmABCG5 was overexpressed and reduced when GmABCG5 was inhibited under iron deficiency. These results showed that the response mechanism to iron deficiency is more actively mobilized in GmABCG5 overexpression seedlings. Our results indicated that GmABCG5 could improve the plant's tolerance to iron deficiency, suggesting that GmABCG5 might have the function of Fe mobilization, redistribution, and/or secretion of Fe substances in plants. The findings provide new insights into the ABCG subfamily genes in the regulation of iron homeostasis in plants.

Iron status and root cell morphology of Arabidopsis thaliana as modified by a bacterial ferri-siderophore

We previously provided evidence for the contribution of pyoverdine to the iron nutrition of Arabidopsis. In the present article, we further analyze the mechanisms and physiology of the adaptations underlying plant iron nutrition through Fe(III)-pyoverdine (Fe(III)-pvd). An integrated approach combining microscopy and nanoscale secondary ion mass spectrometry (NanoSIMS) on plant samples was adopted to localize pyoverdine in planta and assess the impact of this siderophore on the plant iron status and root cellular morphology. The results support a possible plant uptake mechanism of the Fe(III)-pvd complex by epidermal root cells via a non-reductive process associated with the presence of more vesicles. Pyoverdine was transported to the central cylinder via the symplastic and/or trans-cellular pathway(s), suggesting a possible root-to-shoot translocation. All these processes led to enhanced plant iron nutrition, as previously shown. Overall, these findings suggest that bacterial siderophores contribute to plant iron uptake and homeostasis.

A chromosome-scale genome of Peucedanum praeruptorum provide insights into Apioideae evolution and medicinal ingredient biosynthesis

Peucedanum praeruptorum Dunn, a traditional Chinese medicine rich in coumarin, belongs to the Apiaceae family. A high-quality assembled genome of P. praeruptorum is lacking, which has posed obstacles to functional identification and molecular evolution studies of genes associated with coumarin production. Here, a chromosome-scale reference genome of P. praeruptorum, an important medicinal and aromatic plant, was first sequenced and assembled using Oxford Nanopore Technologies and Hi-C sequencing. The final assembled genome size was 1.83 Gb, with a contig N50 of 11.12 Mb. The entire BUSCO evaluation and second-generation read comparability rates were 96.0 % and 99.31 %, respectively. Furthermore, 99.91 % of the genome was anchored to 11 pseudochromosomes. The comparative genomic study revealed the presence of 18,593 orthogroups, which included 476 species-specific orthogroups and 1211 expanded gene families. Two whole-genome duplication (WGD) events and one whole-genome triplication (WGT) event occurred in P. praeruptorum. In addition to the γ-WGT shared by core eudicots or most eudicots, the first WGD was shared by Apiales, while the most recent WGD was unique to Apiaceae. Our study demonstrated that WGD events that occurred in Apioideae highlighted the important role of tandem duplication in the biosynthesis of coumarins and terpenes in P. praeruptorum. Additionally, the expansion of the cytochrome P450 monooxygenase, O-methyltransferase, ATP-binding cassette (ABC) transporter, and terpene synthase families may be associated with the abundance of coumarins and terpenoids. Moreover, we identified >170 UDP-glucosyltransferase members that may be involved in the glycosylation post-modification of coumarins. Significant gene expansion was observed in the ABCG, ABCB, and ABCC subgroups of the ABC transporter family, potentially facilitating the transmembrane transport of coumarins after bolting. The P. praeruptorum genome provides valuable insights into the machinery of coumarin biosynthesis and enhances our understanding of Apiaceae evolution.

Engineered coumarin accumulation reduces mycotoxin-induced oxidative stress and disease susceptibility

Coumarins can fight pathogens and are thus promising for crop protection. Their biosynthesis, however, has not yet been engineered in crops. We tailored the constitutive accumulation of coumarins in transgenic Nicotiana benthamiana, Glycine max and Arabidopsis thaliana plants, as well as in Nicotiana tabacum BY-2 suspension cells. We did so by overexpressing A. thaliana feruloyl-CoA 6-hydroxylase 1 (AtF6'H1), encoding the key enzyme of scopoletin biosynthesis. Besides scopoletin and its glucoside scopolin, esculin at low level was the only other coumarin detected in transgenic cells. Mechanical damage of scopolin-accumulating tissue led to a swift release of scopoletin, presumably from the scopolin pool. High scopolin levels in A. thaliana roots coincided with reduced susceptibility to the root-parasitic nematode Heterodera schachtii. In addition, transgenic soybean plants were more tolerant to the soil-borne pathogenic fungus Fusarium virguliforme. Because mycotoxin-induced accumulation of reactive oxygen species and cell death were reduced in the AtF6'H1-overexpressors, the weaker sensitivity to F. virguliforme may be caused by attenuated oxidative damage of coumarin-hyperaccumulating cells. Together, engineered coumarin accumulation is promising for enhanced disease resilience of crops.

Melatonin Promotes Iron Reactivation and Reutilization in Peach Plants under Iron Deficiency

The yellowing of leaves due to iron deficiency is a prevalent issue in peach production. Although the capacity of exogenous melatonin (MT) to promote iron uptake in peach plants has been demonstrated, its underlying mechanism remains ambiguous. This investigation was carried out to further study the effects of exogenous MT on the iron absorption and transport mechanisms of peach (Prunus persica) plants under iron-deficient conditions through transcriptome sequencing. Under both iron-deficient and iron-supplied conditions, MT increased the content of photosynthetic pigments in peach leaves and decreased the concentrations of pectin, hemicellulose, cell wall iron, pectin iron, and hemicellulose iron in peach plants to a certain extent. These effects stemmed from the inhibitory effect of MT on the polygalacturonase (PG), cellulase (Cx), phenylalanine ammonia-lyase (PAL), and cinnamoyl-coenzyme A reductase (CCR) activities, as well as the promotional effect of MT on the cinnamic acid-4-hydroxylase (C4H) activity, facilitating the reactivation of cell wall component iron. Additionally, MT increased the ferric-chelate reductase (FCR) activity and the contents of total and active iron in various organs of peach plants under iron-deficient and iron-supplied conditions. Transcriptome analysis revealed that the differentially expressed genes (DEGs) linked to iron metabolism in MT-treated peach plants were primarily enriched in the aminoacyl-tRNA biosynthesis pathway under iron-deficient conditions. Furthermore, MT influenced the expression levels of these DEGs, regulating cell wall metabolism, lignin metabolism, and iron translocation within peach plants. Overall, the application of exogenous MT promotes the reactivation and reutilization of iron in peach plants.

Transcription factors dealing with Iron-deficiency stress in plants: focus on the bHLH transcription factor family

Iron (Fe), as an important micronutrient element necessary for plant growth and development, not only participates in multiple physiological and biochemical reactions in cells but also exerts a crucial role in respiration and photosynthetic electron transport. Since Fe is mainly present in the soil in the form of iron hydroxide, Fe deficiency exists universally in plants and has become an important factor triggering crop yield reduction and quality decline. It has been shown that transcription factors (TFs), as an important part of plant signaling pathways, not only coordinate the internal signals of different interaction partners during plant development, but also participate in plant responses to biological and abiotic stresses, such as Fe deficiency stress. Here, the role of bHLH transcription factors in the regulation of Fe homeostasis (mainly Fe uptake) is discussed with emphasis on the functions of MYB, WRKY and other TFs in the maintenance of Fe homeostasis. This review provides a theoretical basis for further studies on the regulation of TFs in Fe deficiency stress response.

Multilayered regulation of iron homeostasis in Arabidopsis

Iron (Fe) is an essential micronutrient for plant growth and development due to its role in crucial processes such as photosynthesis and modulation of the redox state as an electron donor. While Fe is one of the five most abundant metals in the Earth's crust, it is poorly accessible to plants in alkaline soils due to the formation of insoluble complexes. To limit Fe deficiency symptoms, plant have developed a highly sophisticated regulation network including Fe sensing, transcriptional regulation of Fe-deficiency responsive genes, and post-translational modifications of Fe transporters. In this mini-review, we detail how plants perceive intracellular Fe status and how they regulate transporters involved in Fe uptake through a complex cascade of transcription factors. We also describe the current knowledge about intracellular trafficking, including secretion to the plasma membrane, endocytosis, recycling, and degradation of the two main Fe transporters, IRON-REGULATED TRANSPORTER 1 (IRT1) and NATURAL RESISTANCE ASSOCIATED MACROPHAGE PROTEIN 1 (NRAMP1). Regulation of these transporters by their non-Fe substrates is discussed in relation to their functional role to avoid accumulation of these toxic metals during Fe limitation.

Beyond iron-storage pool: functions of plant apoplastic iron during stress

Iron (Fe) is an essential micronutrient for plants, and its storage in the apoplast represents an important Fe pool. Plants have developed various strategies to reutilize this apoplastic Fe pool to adapt to Fe deficiency. In addition, growing evidence indicates that the dynamic changes in apoplastic Fe are critical for plant adaptation to other stresses, including ammonium stress, phosphate deficiency, and pathogen attack. In this review, we discuss and scrutinize the relevance of apoplastic Fe for plant behavior changes in response to stress cues. We mainly focus on the relevant components that modulate the actions and downstream events of apoplastic Fe in stress signaling networks.

Black sheep, dark horses, and colorful dogs: a review on the current state of the Gene Ontology with respect to iron homeostasis in Arabidopsis thaliana

Cellular homeostasis of the micronutrient iron is highly regulated in plants and responsive to nutrition, stress, and developmental signals. Genes for iron management encode metal and other transporters, enzymes synthesizing chelators and reducing substances, transcription factors, and several types of regulators. In transcriptome or proteome datasets, such iron homeostasis-related genes are frequently found to be differentially regulated. A common method to detect whether a specific cellular pathway is affected in the transcriptome data set is to perform Gene Ontology (GO) enrichment analysis. Hence, the GO database is a widely used resource for annotating genes and identifying enriched biological pathways in Arabidopsis thaliana. However, iron homeostasis-related GO terms do not consistently reflect gene associations and levels of evidence in iron homeostasis. Some genes in the existing iron homeostasis GO terms lack direct evidence of involvement in iron homeostasis. In other aspects, the existing GO terms for iron homeostasis are incomplete and do not reflect the known biological functions associated with iron homeostasis. This can lead to potential errors in the automatic annotation and interpretation of GO term enrichment analyses. We suggest that applicable evidence codes be used to add missing genes and their respective ortholog/paralog groups to make the iron homeostasis-related GO terms more complete and reliable. There is a high likelihood of finding new iron homeostasis-relevant members in gene groups and families like the ZIP, ZIF, ZIFL, MTP, OPT, MATE, ABCG, PDR, HMA, and HMP. Hence, we compiled comprehensive lists of genes involved in iron homeostasis that can be used for custom enrichment analysis in transcriptomic or proteomic studies, including genes with direct experimental evidence, those regulated by central transcription factors, and missing members of small gene families or ortholog/paralog groups. As we provide gene annotation and literature alongside, the gene lists can serve multiple computational approaches. In summary, these gene lists provide a valuable resource for researchers studying iron homeostasis in A. thaliana, while they also emphasize the importance of improving the accuracy and comprehensiveness of the Gene Ontology.

ELONGATED HYPOCOTYL 5 regulates BRUTUS and affects iron acquisition and homeostasis in Arabidopsis thaliana

Iron (Fe) is an essential micronutrient for both plants and animals. Fe-limitation significantly reduces crop yield and adversely impacts on human nutrition. Owing to limited bioavailability of Fe in soil, plants have adapted different strategies that not only regulate Fe-uptake and homeostasis but also bring modifications in root system architecture to enhance survival. Understanding the molecular mechanism underlying the root growth responses will have critical implications for plant breeding. Fe-uptake is regulated by a cascade of basic helix-loop-helix (bHLH) transcription factors (TFs) in plants. In this study, we report that HY5 (Elongated Hypocotyl 5), a member of the basic leucine zipper (bZIP) family of TFs, plays an important role in the Fe-deficiency signaling pathway in Arabidopsis thaliana. The hy5 mutant failed to mount optimum Fe-deficiency responses, and displayed root growth defects under Fe-limitation. Our analysis revealed that the induction of the genes involved in Fe-uptake pathway (FIT-FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR, FRO2-FERRIC REDUCTION OXIDASE 2 and IRT1-IRON-REGULATED TRANSPORTER1) is reduced in the hy5 mutant as compared with the wild-type plants under Fe-deficiency. Moreover, we also found that the expression of coumarin biosynthesis genes is affected in the hy5 mutant under Fe-deficiency. Our results also showed that HY5 negatively regulates BRUTUS (BTS) and POPEYE (PYE). Chromatin immunoprecipitation followed by quantitative polymerase chain reaction revealed direct binding of HY5 to the promoters of BTS, FRO2 and PYE. Altogether, our results showed that HY5 plays an important role in the regulation of Fe-deficiency responses in Arabidopsis.

Impact of soybean-associated plant growth-promoting bacteria on plant growth modulation under alkaline soil conditions

Conventional strategies to manage iron (Fe) deficiency still present drawbacks, and more eco-sustainable solutions are needed. Knowledge on soybean-specific diversity and functional traits of their plant growth-promoting bacteria (PGPB) potentiates their applicability as bioinoculants to foster soybean performance under calcareous soil conditions. This work aimed to assess the efficacy of PGPB, retrieved from soybean tissues/rhizosphere, in enhancing plant growth and development as well as crop yield under alkaline soil conditions. Seventy-six bacterial strains were isolated from shoots (18%), roots (53%), and rhizosphere (29%) of soybean. Twenty-nine genera were identified, with Bacillus and Microbacterium being the most predominant. Based on distinct plant growth-promoting traits, the endophyte Bacillus licheniformis P2.3 and the rhizobacteria Bacillus aerius S2.14 were selected as bioinoculants. In vivo tests showed that soybean photosynthetic parameters, chlorophyll content, total fresh weight, and Fe concentrations were not significantly affected by bioinoculation. However, inoculation with B. licheniformis P2.3 increased pod number (33%) and the expression of Fe-related genes (FRO2, IRT1, F6'H1, bHLH38, and FER4), and decreased FC-R activity (45%). Moreover, bioinoculation significantly affected Mn, Zn, and Ca accumulation in plant tissues. Soybean harbors several bacterial strains in their tissues and in the rhizosphere with capacities related to Fe nutrition and plant growth promotion. The strain B. licheniformis P2.3 showed the best potential to be incorporated in bioinoculant formulations for enhancing soybean performance under alkaline soil conditions.

Indole-3-acetaldoxime delays root iron-deficiency responses and modify auxin homeostasis in Medicago truncatula

Iron (Fe) is an essential plant micronutrient, being a major limiting growth factor in calcareous soils. To increase Fe uptake, plants induce lateral roots growth, the expression of a Fe(III)-chelate reductase (FCR), a Fe(II)-transporter and a H⁺-ATPase and the secretion of flavins. Furthermore, auxin hormone family is involved in the Fe-deficiency responses but the action mechanism remains elusive. In this work, we evaluated the effect of the auxin-precursor indole-3-acetaldoxime (IAOx) on hydroponically grown Medicago truncatula plants under different Fe conditions. Upon 4-days of Fe starvation, the pH of the nutrient solution decreased, while both the FCR activity and the presence of flavins increased. Exogenous IAOx increased lateral roots growth contributing to superroot phenotype, decreased chlorosis, and delayed up to 3-days the pH-decrease, the FCR-activity increase, and the presence of flavins, compared to Fe-deficient plants. Gene expression levels were in concordance with the physiological responses. RESULTS: showed that IAOx was immediately transformed to IAN in roots and shoots to maintain auxin homeostasis. IAOx plays an active role in iron homeostasis delaying symptoms and responses in Fe-deficient plants. We may speculate that IAOx or its derivatives remobilize Fe from root cells to alleviate Fe-deficiency. Overall, these results point out that the IAOx-derived phenotype may have advantages to overcome nutritional stresses.

The chemical ecology of coumarins and phenazines affects iron acquisition by pseudomonads

Secondary metabolites are important facilitators of plant-microbe interactions in the rhizosphere, contributing to communication, competition, and nutrient acquisition. However, at first glance, the rhizosphere seems full of metabolites with overlapping functions, and we have a limited understanding of basic principles governing metabolite use. Increasing access to the essential nutrient iron is one important, but seemingly redundant role performed by both plant and microbial Redox-Active Metabolites (RAMs). We used coumarins, RAMs made by the model plant Arabidopsis thaliana, and phenazines, RAMs made by soil-dwelling pseudomonads, to ask whether plant and microbial RAMs might each have distinct functions under different environmental conditions. We show that variations in oxygen and pH lead to predictable differences in the capacity of coumarins vs phenazines to increase the growth of iron-limited pseudomonads and that these effects depend on whether pseudomonads are grown on glucose, succinate, or pyruvate: carbon sources commonly found in root exudates. Our results are explained by the chemical reactivities of these metabolites and the redox state of phenazines as altered by microbial metabolism. This work shows that variations in the chemical microenvironment can profoundly affect secondary metabolite function and suggests plants may tune the utility of microbial secondary metabolites by altering the carbon released in root exudates. Together, these findings suggest that RAM diversity may be less overwhelming when viewed through a chemical ecological lens: Distinct molecules can be expected to be more or less important to certain ecosystem functions, such as iron acquisition, depending on the local chemical microenvironments in which they reside.

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.

Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters

ABCG46 of the legume Medicago truncatula is an ABC-type transporter responsible for highly selective translocation of the phenylpropanoids, 4-coumarate, and liquiritigenin, over the plasma membrane. To investigate molecular determinants of the observed substrate selectivity, we applied a combination of phylogenetic and biochemical analyses, AlphaFold2 structure prediction, molecular dynamics simulations, and mutagenesis. We discovered an unusually narrow transient access path to the central cavity of MtABCG46 that constitutes an initial filter responsible for the selective translocation of phenylpropanoids through a lipid bilayer. Furthermore, we identified remote residue F562 as pivotal for maintaining the stability of this filter. The determination of individual amino acids that impact the selective transport of specialized metabolites may provide new opportunities associated with ABCGs being of interest, in many biological scenarios.

Biotic stress-induced changes in root exudation confer plant stress tolerance by altering rhizospheric microbial community

Every organism on the earth maintains some kind of interaction with its neighbours. As plants are sessile, they sense the varied above-ground and below-ground environmental stimuli and decipher these dialogues to the below-ground microbes and neighbouring plants via root exudates as chemical signals resulting in the modulation of the rhizospheric microbial community. The composition of root exudates depends upon the host genotype, environmental cues, and interaction of plants with other biotic factors. Crosstalk of plants with biotic agents such as herbivores, microbes, and neighbouring plants can change host plant root exudate composition, which may permit either positive or negative interactions to generate a battlefield in the rhizosphere. Compatible microbes utilize the plant carbon sources as their organic nutrients and show robust co-evolutionary changes in changing circumstances. In this review, we have mainly focused on the different biotic factors responsible for the synthesis of alternative root exudate composition leading to the modulation of rhizosphere microbiota. Understanding the stress-induced root exudate composition and resulting change in microbial community can help us to devise strategies in engineering plant microbiomes to enhance plant adaptive capabilities in a stressful environment.

Iron sensing in plants

The ease of accepting or donating electrons is the raison d'être for the pivotal role iron (Fe) plays in a multitude of vital processes. In the presence of oxygen, however, this very property promotes the formation of immobile Fe(III) oxyhydroxides in the soil, which limits the concentration of Fe that is available for uptake by plant roots to levels well below the plant's demand. To adequately respond to a shortage (or, in the absence of oxygen, a possible surplus) in Fe supply, plants have to perceive and decode information on both external Fe levels and the internal Fe status. As a further challenge, such cues have to be translated into appropriate responses to satisfy (but not overload) the demand of sink (i.e., non-root) tissues. While this seems to be a straightforward task for evolution, the multitude of possible inputs into the Fe signaling circuitry suggests diversified sensing mechanisms that concertedly contribute to govern whole plant and cellular Fe homeostasis. Here, we review recent progress in elucidating early events in Fe sensing and signaling that steer downstream adaptive responses. The emerging picture suggests that Fe sensing is not a central event but occurs in distinct locations linked to distinct biotic and abiotic signaling networks that together tune Fe levels, Fe uptake, root growth, and immunity in an interwoven manner to orchestrate and prioritize multiple physiological readouts.

Ferrous iron uptake via IRT1/ZIP evolved at least twice in green plants

Iron (Fe) is essential for virtually all organisms, being irreplaceable because of its electrochemical properties that enable many biochemical processes, including photosynthesis. Besides its abundance, Fe is generally found in the poorly soluble form of ferric iron (Fe³⁺ ), while most plants uptake the soluble form Fe²⁺ . The model angiosperm Arabidopsis thaliana, for example, captures Fe through a mechanism that lowers rhizosphere pH through proton pumping that increases Fe³⁺ solubility, which is then reduced by a membrane-bound reductase and transported into the cell by the zinc-regulated, iron-regulated transporter-like protein (ZIP) family protein AtIRT1. ZIP proteins are transmembrane transporters of divalent metals such as Fe²⁺ , Zn²⁺ , Mn²⁺ , and Cd²⁺ . In this work, we investigated the evolution of functional homologs of IRON-REGULATED TRANSPORTER 1/ZIP in the supergroup Archaeplastida (Viridiplantae + Rhodophyta + Glaucophyta) using 51 genomes of diverse lineages. Our analyses suggest that Fe is acquired through deeply divergent ZIP proteins in land plants and chlorophyte green algae, indicating that Fe²⁺ uptake by ZIP proteins evolved independently at least twice throughout green plant evolution. Our results indicate that the archetypical IRON-REGULATED TRANSPORTER (IRT) proteins from angiosperms likely emerged before the origin of land plants during early streptophyte algae terrestrialization, a process that required the evolution of Fe acquisition in terrestrial subaerial settings.

Entomopathogenic Fungi-Mediated Solubilization and Induction of Fe Related Genes in Melon and Cucumber Plants

Endophytic insect pathogenic fungi have a multifunctional lifestyle; in addition to its well-known function as biocontrol agents, it may also help plants respond to other biotic and abiotic stresses, such as iron (Fe) deficiency. This study explores M. brunneum EAMa 01/58-Su strain attributes for Fe acquisition. Firstly, direct attributes include siderophore exudation (in vitro assay) and Fe content in shoots and in the substrate (in vivo assay) were evaluated for three strains of Beauveria bassiana and Metarhizium bruneum. The M. brunneum EAMa 01/58-Su strain showed a great ability to exudate iron siderophores (58.4% surface siderophores exudation) and provided higher Fe content in both dry matter and substrate compared to the control and was therefore selected for further research to unravel the possible induction of Fe deficiency responses, Ferric Reductase Activity (FRA), and relative expression of Fe acquisition genes by qRT-PCR in melon and cucumber plants.. In addition, root priming by M. brunneum EAMa 01/58-Su strain elicited Fe deficiency responses at transcriptional level. Our results show an early up-regulation (24, 48 or 72 h post inoculation) of the Fe acquisition genes FRO1, FRO2, IRT1, HA1, and FIT as well as the FRA. These results highlight the mechanisms involved in the Fe acquisition as mediated by IPF M. brunneum EAMa 01/58-Su strain.

Molecular and physiological mechanisms of tea (Camellia sinensis (L.) O. Kuntze) leaf and root in response to nitrogen deficiency

BACKGROUND

As an economically important crop, tea is strongly nitrogen (N)-dependent. However, the physiological and molecular mechanisms underlying the response of N deficiency in tea are not fully understood. Tea cultivar "Chunlv2" [Camellia sinensis (L.) O. Kuntze] were cultured with a nutrient solution with 0 mM [N-deficiency] or 3 mM (Control) NH₄NO₃ in 6 L pottery pots containing clean river sands.

RESULTS

N deficiency significantly decreased N content, dry weight, chlorophyll (Chl) content, L-theanine and the activities of N metabolism-related enzymes, but increased the content of total flavonoids and polyphenols in tea leaves. N deficiency delayed the sprouting time of tea buds. By using the RNA-seq technique and subsequent bioinformatics analysis, 3050 up-regulated and 2688 down-regulated differentially expressed genes (DEGs) were isolated in tea leaves in response to N deficiency. However, only 1025 genes were up-regulated and 744 down-regulated in roots. Gene ontology (GO) term enrichment analysis showed that 205 DEGs in tea leaves were enriched in seven GO terms and 152 DEGs in tea roots were enriched in 11 GO items based on P < 0.05. In tea leaves, most GO-enriched DEGs were involved in chlorophyll a/b binding activities, photosynthetic performance, and transport activities. But most of the DEGs in tea roots were involved in the metabolism of carbohydrates and plant hormones with regard to the GO terms of biological processes. N deficiency significantly increased the expression level of phosphate transporter genes, which indicated that N deficiency might impair phosphorus metabolism in tea leaves. Furthermore, some DEGs, such as probable anion transporter 3 and high-affinity nitrate transporter 2.7, might be of great potential in improving the tolerance of N deficiency in tea plants and further study could work on this area in the future.

CONCLUSIONS

Our results indicated N deficiency inhibited the growth of tea plant, which might be due to altered N metabolism and expression levels of DEGs involved in the photosynthetic performance, transport activity and oxidation-reduction processes.

Iron Nutrition in Plants: Towards a New Paradigm?

Iron (Fe) is an essential micronutrient for plant growth and development. Fe availability affects crops' productivity and the quality of their derived products and thus human nutrition. Fe is poorly available for plant use since it is mostly present in soils in the form of insoluble oxides/hydroxides, especially at neutral to alkaline pH. How plants cope with low-Fe conditions and acquire Fe from soil has been investigated for decades. Pioneering work highlighted that plants have evolved two different strategies to mine Fe from soils, the so-called Strategy I (Fe reduction strategy) and Strategy II (Fe chelation strategy). Strategy I is employed by non-grass species whereas graminaceous plants utilize Strategy II. Recently, it has emerged that these two strategies are not fully exclusive and that the mechanism used by plants for Fe uptake is directly shaped by the characteristics of the soil on which they grow (e.g., pH, oxygen concentration). In this review, recent findings on plant Fe uptake and the regulation of this process will be summarized and their impact on our understanding of plant Fe nutrition will be discussed.

Specialized metabolites as versatile tools in shaping plant-microbe associations

Plants are rich repository of a large number of chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes including responses against changing abiotic conditions and interactions with various co-existing organisms. One of the strikingly affirmed functions of these specialized metabolites is their involvement in plants' life-long interactions with complex multi-kingdom microbiomes including both beneficial and harmful microorganisms. Recent developments in genomic and molecular biology tools not only help to generate well-curated information about regulatory and structural components of biosynthetic pathways of plant specialized metabolites but also to create and screen mutant lines defective in their synthesis. In this review, we have comprehensively surveyed the function of these specialized metabolites and discussed recent research findings demonstrating the responses of various microbes on tested mutant lines having defective biosynthesis of particular metabolites. In addition, we attempt to provide key clues about the impact of these metabolites on the assembly of the plant microbiome by summarizing the major findings of recent comparative metagenomic analyses of available mutant lines under customized and natural microbial niches. Subsequently, we delineate benchmark initiatives that aim to engineer or manipulate the biosynthetic pathways to produce specialized metabolites in heterologous systems but also to diversify their immune function. While denoting the function of these metabolites, we also discuss the critical bottlenecks associated with understanding and exploiting their function in improving plant adaptation to the environment.

Iron Availability and Homeostasis in Plants: A Review of Responses, Adaptive Mechanisms, and Signaling

Iron is an essential element for all living organisms, playing a major role in plant biochemistry as a redox catalyst based on iron redox properties. Iron is the fourth most abundant element of the Earth's crust, but its uptake by plants is complex because it is often in insoluble forms that are not easily accessible for plants to use. The physical and chemical speciation of iron, as well as rhizosphere activity, are key factors controlling the bioavailability of Fe. Iron can be under reduced (Fe²⁺) or oxidized (Fe³⁺) ionic forms, adsorbed onto mineral surfaces, forming complexes with organic molecules, precipitated to form poorly crystalline hydroxides to highly crystalline iron oxides, or included in crystalline Fe-rich mineral phases. Plants must thus adapt to a complex and changing iron environment, and their response is finely regulated by multiple signaling pathways initiated by a diversity of stimulus perceptions. Higher plants possess two separate strategies to uptake iron from rhizosphere soil: the chelation strategy and the reduction strategy in grass and non-grass plants, respectively. Molecular actors involved in iron uptake and mobilization through the plant have been characterized for both strategies. All these processes that contribute to iron homeostasis in plants are highly regulated in response to iron availability by downstream signaling responses, some of which are characteristic signaling signatures of iron dynamics, while others are shared with other environmental stimuli. Recent research has thus revealed key transcription factors, cis-acting elements, post-translational regulators, and other molecular mechanisms controlling these genes or their encoded proteins in response to iron availability. In addition, the most recent research is increasingly highlighting the crosstalk between iron homeostasis and nutrient response regulation. These regulatory processes help to avoid plant iron concentrations building up to potential cell functioning disruptions that could adversely affect plant fitness. Indeed, when iron is in excess in the plant, it can lead to the production and accumulation of dangerous reactive oxygen species and free radicals (H₂O₂, HO^•, O₂^•-, HO^•₂) that can cause considerable damages to most cellular components. To cope with iron oxidative stress, plants have developed defense systems involving the complementary action of antioxidant enzymes and molecular antioxidants, safe iron-storage mechanisms, and appropriate morphological adaptations.

The Use of Spectral Imaging to Follow the Iron and pH-Dependent Accumulation of Fluorescent Coumarins

Plants challenged with iron deficiency produce in their roots and secrete into the rhizosphere several small molecules named coumarins that derive from the phenylpropanoid pathway. Coumarins are biosynthesized in different root cell types and transported to the root epidermis prior to their secretion in the surrounding media. Taking advantage of the natural fluorescence of most coumarins glycosides when exposed to UV light, we developed a method to uncover their individual cellular localization and accumulation. This approach couples spectral imaging acquisition and linear unmixing analysis. In this protocol, we describe guidelines, experimental setup, and conditions for the analysis of coumarins localization and accumulation in Arabidopsis thaliana root seedlings grown in control and iron deficiency conditions, at both acidic and alkaline pH.

Correlation between Perturbation of Redox Homeostasis and Antibiofilm Capacity of Phytochemicals at Non-Lethal Concentrations

Biofilms are the multicellular lifestyle of microorganisms and are present on potentially every type of biotic or abiotic surface. Detrimental biofilms are generally targeted with antimicrobial compounds. Phytochemicals at sub-lethal concentrations seem to be an exciting alternative strategy to control biofilms, as they are less likely to impose selective pressure leading to resistance. This overview gathers the literature on individual phytocompounds rather than on extracts of which the use is difficult to reproduce. To the best of our knowledge, this is the first review to target only individual phytochemicals below inhibitory concentrations against biofilm formation. We explored whether there is an overall mechanism that can explain the effects of individual phytochemicals at sub-lethal concentrations. Interestingly, in all experiments reported here in which oxidative stress was investigated, a modest increase in intracellular reactive oxygen species was reported in treated cells compared to untreated specimens. At sub-lethal concentrations, polyphenolic substances likely act as pro-oxidants by disturbing the healthy redox cycle and causing an accumulation of reactive oxygen species.

Similarities and differences in iron homeostasis strategies between graminaceous and nongraminaceous plants

Iron (Fe) homeostasis is essential for both plant development and human nutrition. The maintenance of Fe homeostasis involves a complex network in which Fe signaling nodes and circuits coordinate tightly Fe transporters, ferric reductases, H⁺ -ATPases, low-molecular-mass metal chelators, and transporters of chelators and Fe-chelate complexes. Early-stage studies have revealed different strategies for Fe homeostasis between graminaceous and nongraminaceous plants. Recent progress has refreshed our understanding of previous knowledge, especially on the uptake, phloem transport and systemic signaling of Fe. This review attempts to summarize recent exciting and potentially influential studies on the various routes of Fe uptake and distribution in plants, focusing on breakthroughs that have changed our understanding of plant Fe nutrition.

The bHLH Transcription Factor OsbHLH057 Regulates Iron Homeostasis in Rice

Many basic Helix-Loop-Helix (bHLH) transcription factors precisely regulate the expression of Fe uptake and translocation genes to control iron (Fe) homeostasis, as both Fe deficiency and toxicity impair plant growth and development. In rice, three clade IVc bHLH transcription factors have been characterised as positively regulating Fe-deficiency response genes. However, the function of OsbHLH057, another clade IVc bHLH transcription factor, in regulating Fe homeostasis is unknown. Here, we report that OsbHLH057 is involved in regulating Fe homeostasis in rice. OsbHLH057 was highly expressed in the leaf blades and lowly expressed in the roots; it was mainly expressed in the stele and highly expressed in the lateral roots. In addition, OsbHLH057 was slightly induced by Fe deficiency in the shoots on the first day but was not affected by Fe availability in the roots. OsbHLH057 localised in the nucleus exhibited transcriptional activation activity. Under Fe-sufficient conditions, OsbHLH057 knockout or overexpression lines increased or decreased the shoot Fe concentration and the expression of several Fe homeostasis-related genes, respectively. Under Fe-deficient conditions, plants with an OsbHLH057 mutation showed susceptibility to Fe deficiency and accumulated lower Fe concentrations in the shoot compared with the wild type. Unexpectedly, the OsbHLH057-overexpressing lines had reduced tolerance to Fe deficiency. These results indicate that OsbHLH057 plays a positive role in regulating Fe homeostasis, at least under Fe-sufficient conditions.

The rhizosphere microbiome: Plant-microbial interactions for resource acquisition

While horticulture tools and methods have been extensively developed to improve the management of crops, systems to harness the rhizosphere microbiome to benefit plant crops are still in development. Plants and microbes have been coevolving for several millennia, conferring fitness advantages that expand the plant's own genetic potential. These beneficial associations allow the plants to cope with abiotic stresses such as nutrient deficiency across a wide range of soils and growing conditions. Plants achieve these benefits by selectively recruiting microbes using root exudates, positively impacting their nutrition, health and overall productivity. Advanced knowledge of the interplay between root exudates and microbiome alteration in response to plant nutrient status, and the underlying mechanisms there of, will allow the development of technologies to increase crop yield. This review summarizes current knowledge and perspectives on plant-microbial interactions for resource acquisition and discusses promising advances for manipulating rhizosphere microbiomes and root exudation.

Mechanistic assessment of tolerance to iron deficiency mediated by Trichoderma harzianum in soybean roots

AIMS

Iron (Fe) deficiency in soil is a continuing problem for soybean (Glycine max L.) production, partly as a result of continuing climate change. This study elucidates how Trichoderma harzianum strain T22 (TH) mitigates growth retardation associated with Fe-deficiency in a highly sensitive soybean cultivar.

METHODS AND RESULTS

Soil TH supplementation led to mycelial colonization and the presence of UAOX1 gene in roots that caused substantial improvement in chlorophyll score, photosynthetic efficiency and morphological parameters, indicating a positive influence on soybean health. Although rhizosphere acidification was found to be a common feature of Fe-deficient soybean, the upregulation of Fe-reductase activity (GmFRO2) and total phenol secretion were two of the mechanisms that substantially increased the Fe availability by TH. Heat-killed TH applied to soil caused no improvement in photosynthetic attributes and Fe-reductase activity, confirming the active role of TH in mitigating Fe-deficiency. Consistent increases in tissue Fe content and increased Fe-transporter (GmIRT1, GmNRAMP2a, GmNRAMP2b and GmNRAMP7) mRNA levels in roots following TH supplementation were observed only under Fe-deprivation. Root cell death, electrolyte leakage, superoxide (O2 •- ) and hydrogen peroxide (H2 O2 ) substantially declined due to TH in Fe-deprived plants. Further, the elevation of citrate and malate concentration along with the expression of citrate synthase (GmCs) and malate synthase (GmMs) caused by TH suggest improved chelation of Fe in Fe-deficient plants. Results also suggest that TH has a role in triggering antioxidant defence by increasing the activity of glutathione reductase (GR) along with elevated S-metabolites (glutathione and methionine) to stabilize redox status under Fe-deficiency.

CONCLUSIONS

TH increases the availability and mobilization of Fe by inducing Fe-uptake pathways, which appears to help provide resistance to oxidative stress associated with Fe-shortage in soybean.

SIGNIFICANCE AND IMPACT OF THE STUDY

These findings indicate that while Fe deficiency does not affect the rate or degree of TH hyphal association in soybean roots, the beneficial effects of TH alone may be Fe deficiency-dependent.

POPEYE intercellular localization mediates cell-specific iron deficiency responses

Plants must tightly regulate iron (Fe) sensing, acquisition, transport, mobilization, and storage to ensure sufficient levels of this essential micronutrient. POPEYE (PYE) is an iron responsive transcription factor that positively regulates the iron deficiency response, while also repressing genes essential for maintaining iron homeostasis. However, little is known about how PYE plays such contradictory roles. Under iron-deficient conditions, pPYE:GFP accumulates in the root pericycle while pPYE:PYE-GFP is localized to the nucleus in all Arabidopsis (Arabidopsis thaliana) root cells, suggesting that PYE may have cell-specific dynamics and functions. Using scanning fluorescence correlation spectroscopy and cell-specific promoters, we found that PYE-GFP moves between different cells and that the tendency for movement corresponds with transcript abundance. While localization to the cortex, endodermis, and vasculature is required to manage changes in iron availability, vasculature and endodermis localization of PYE-GFP protein exacerbated pye-1 defects and elicited a host of transcriptional changes that are detrimental to iron mobilization. Our findings indicate that PYE acts as a positive regulator of iron deficiency response by regulating iron bioavailability differentially across cells, which may trigger iron uptake from the surrounding rhizosphere and impact root energy metabolism.

Iron uptake, signaling, and sensing in plants

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

ATP-Binding Cassette G Transporters and Their Multiple Roles Especially for Male Fertility in Arabidopsis, Rice and Maize

ATP-binding cassette subfamily G (ABCG) transporters are extensive in plants and play essential roles in various processes influencing plant fitness, but the research progress varies greatly among Arabidopsis, rice and maize. In this review, we present a consolidated nomenclature and characterization of the whole 51 ABCG transporters in maize, perform a phylogenetic analysis and classification of the ABCG subfamily members in maize, and summarize the latest research advances in ABCG transporters for these three plant species. ABCG transporters are involved in diverse processes in Arabidopsis and rice, such as anther and pollen development, vegetative and female organ development, abiotic and biotic stress response, and phytohormone transport, which provide useful clues for the functional investigation of ABCG transporters in maize. Finally, we discuss the current challenges and future perspectives for the identification and mechanism analysis of substrates for plant ABCG transporters. This review provides a basic framework for functional research and the potential application of ABCG transporters in multiple plants, including maize.

Genome Editing Targets for Improving Nutrient Use Efficiency and Nutrient Stress Adaptation

In recent years, the development of RNA-guided genome editing (CRISPR-Cas9 technology) has revolutionized plant genome editing. Under nutrient deficiency conditions, different transcription factors and regulatory gene networks work together to maintain nutrient homeostasis. Improvement in the use efficiency of nitrogen (N), phosphorus (P) and potassium (K) is essential to ensure sustainable yield with enhanced quality and tolerance to stresses. This review outlines potential targets suitable for genome editing for understanding and improving nutrient use (NtUE) efficiency and nutrient stress tolerance. The different genome editing strategies for employing crucial negative and positive regulators are also described. Negative regulators of nutrient signalling are the potential targets for genome editing, that may improve nutrient uptake and stress signalling under resource-poor conditions. The promoter engineering by CRISPR/dead (d) Cas9 (dCas9) cytosine and adenine base editing and prime editing is a successful strategy to generate precise changes. CRISPR/dCas9 system also offers the added advantage of exploiting transcriptional activators/repressors for overexpression of genes of interest in a targeted manner. CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) are variants of CRISPR in which a dCas9 dependent transcription activation or interference is achieved. dCas9-SunTag system can be employed to engineer targeted gene activation and DNA methylation in plants. The development of nutrient use efficient plants through CRISPR-Cas technology will enhance the pace of genetic improvement for nutrient stress tolerance of crops and improve the sustainability of agriculture.

Altered metal distribution in the sr45-1 Arabidopsis mutant causes developmental defects

The plant serine/arginine-rich (SR) splicing factor SR45 plays important roles in several biological processes, such as splicing, DNA methylation, innate immunity, glucose regulation, and abscisic acid signaling. A homozygous Arabidopsis sr45-1 null mutant is viable, but exhibits diverse phenotypic alterations, including delayed root development, late flowering, shorter siliques with fewer seeds, narrower leaves and petals, and unusual numbers of floral organs. Here, we report that the sr45-1 mutant presents an unexpected constitutive iron deficiency phenotype characterized by altered metal distribution in the plant. RNA-Sequencing highlighted severe perturbations in metal homeostasis, the phenylpropanoid pathway, oxidative stress responses, and reproductive development. Ionomic quantification and histochemical staining revealed strong iron accumulation in the sr45-1 root tissues accompanied by iron starvation in aerial parts. Mis-splicing of several key iron homeostasis genes, including BTS, bHLH104, PYE, FRD3, and ZIF1, was observed in sr45-1 roots. We showed that some sr45-1 developmental abnormalities can be complemented by exogenous iron supply. Our findings provide new insight into the molecular mechanisms governing the phenotypes of the sr45-1 mutant.

Comparative Transcriptomics Unveil the Crucial Genes Involved in Coumarin Biosynthesis in Peucedanum praeruptorum Dunn

Peucedanum praeruptorum Dunn is a commonly used traditional Chinese medicine that is abundant in furano- and dihydropyrano coumarins. When P. praeruptorum reaches the bolting stage, the roots gradually lignified, and the content of coumarins declines rapidly. Non-bolting has always been a decisive factor for harvesting the P. praeruptorum materials. To evaluate the amount of coumarin components in unbolted and bolted P. praeruptorum, the variations of praeruptorin A, praeruptorin B, praeruptorin E, peucedanocoumarin I, and peucedanocoumarin II were determined. Additionally, 336,505 transcripts were obtained from the comparative transcriptome data. Among them, a total of 1,573 differentially expressed genes were screened out. To identify the critical genes involved in coumarin biosynthesis, comparative transcriptomics coupled with co-expression associated analysis was conducted. Finally, coumarin biosynthesis-related eighteen candidate genes were selected for the validation of qPCR. Additionally, a phylogenetic tree and the expression profile of ATP-binding cassette (ABC) transporters were constructed. To clarify the main genes in the regulation of coumarin biosynthesis, the interaction network of the co-expression genes from thirteen modules was constructed. Current results exhibited the significant increment of praeruptorin A, praeruptorin B and praeruptorin E in the bolted P. praeruptorum. Although, peucedanocoumarin I and peucedanocoumarin II were slightly increased. Besides the content of coumarins, the essential genes involved in the coumarin biosynthesis also exhibited an overall downward trend after bolting. Three peroxidases (PRXs) involved in the production of lignin monomers had been demonstrated to be downregulated. PAL, C4H, HCT, COMT, CCoAOMT, and some ABC transporters were dramatically downregulated at the bolting stage. These results indicated that the downregulation of coumarin biosynthetic genes in the bolted P. praeruptorum ultimately reduced the formation of coumarins. However, the mechanism through which bolting indirectly affects the formation of coumarin still needs extra functional verification.

Enantioselective Response of Wheat Seedlings to Imazethapyr: From the Perspective of Fe and the Secondary Metabolite DIMBOA

The responses of trace elements and secondary metabolites to stress can reflect plant adaptation to the environment. If and how the imperative trace element Fe and the defensive secondary metabolite 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazine-3(4H)-one (DIMBOA) mediate the toxicity of chiral herbicides to nontarget plants remains inconclusive. We found that the herbicidal-active imazethapyr enantiomer [(R)-IM] stimulated heme oxygenase-1 activity, triggered the release of the catalytic product Fe²⁺, increased reactive oxygen species production, decreased the DIMBOA content, and increased the DIMBOA-Fe content. XAFS analyses and in vitro Fenton assays demonstrated that DIMBOA could relieve phytotoxicity by chelating excessive Fe³⁺ to restore Fe homeostasis. The free radical scavenging ability of the chelate of DIMBOA and Fe was also involved. This work refines the dual role of DIMBOA and Fe in mediating the enantioselective phytotoxicity of chiral herbicides, which provides a new direction for improving the herbicide resistance of crops.

The ins and outs of transporters at plasma membrane and tonoplast in plant specialized metabolism

Covering: up to 2022Plants are organic chemists par excellence and produce an amazing array of diverse chemical structures. Whereas primary metabolites are essential for all living organisms and highly conserved, the specialized metabolites constitute the taxonomy-specific chemical languages that are key for fitness and survival. Allocation of plants' wide array of specialized metabolites in patterns that are fine-tuned spatiotemporally is essential for adaptation to the ever-changing environment and requires transport processes. Thus advancing our knowledge about transporters is important as also evidenced by the increasing number of transporters that control key quality traits in agriculture. In this review, we will highlight recently identified transporters and new insights related to already known transporters of plant specialized metabolites. Focus will be on the transport mechanism revealed by the biochemical characterization and how that links to its function in planta.

Effects of Fe and Mn Deficiencies on the Root Protein Profiles of Tomato (Solanum lycopersicum) Using Two-Dimensional Electrophoresis and Label-Free Shotgun Analyses

Iron (Fe) and manganese (Mn) are two essential elements for plants that compete for the same uptake transporters and show conflicting interactions at the regulatory level. In order to understand the differential response to both metal deficiencies in plants, two proteomic techniques (two-dimensional gel electrophoresis and label-free shotgun) were used to study the proteome profiles of roots from tomato plants grown under Fe or Mn deficiency. A total of 119 proteins changing in relative abundance were confidently quantified and identified, including 35 and 91 in the cases of Fe deficiency and Mn deficiency, respectively, with 7 of them changing in both deficiencies. The identified proteins were categorized according to function, and GO-enrichment analysis was performed. Data showed that both deficiencies provoked a common and intense cell wall remodelling. However, the response observed for Fe and Mn deficiencies differed greatly in relation to oxidative stress, coumarin production, protein, nitrogen, and energy metabolism.

Plant iron nutrition: the long road from soil to seeds

Iron (Fe) is an essential plant micronutrient since many cellular processes including photosynthesis, respiration, and the scavenging of reactive oxygen species depend on adequate Fe levels; however, non-complexed Fe ions can be dangerous for cells, as they can act as pro-oxidants. Hence, plants possess a complex homeostatic control system for safely taking up Fe from the soil and transporting it to its various cellular destinations, and for its subcellular compartmentalization. At the end of the plant's life cycle, maturing seeds are loaded with the required amount of Fe needed for germination and early seedling establishment. In this review, we discuss recent findings on how the microbiota in the rhizosphere influence and interact with the strategies adopted by plants to take up iron from the soil. We also focus on the process of seed-loading with Fe, and for crop species we also consider its associated metabolism in wild relatives. These two aspects of plant Fe nutrition may provide promising avenues for a better comprehension of the long pathway of Fe from soil to seeds.

Toward understanding the genetic bases underlying plant-mediated "cry for help" to the microbiota

Canonical plant stress biology research has focused mainly on the dynamic regulation of internal genetic pathways in stress responses. Increasingly more studies suggest that plant-mediated timely reshaping of the microbiota could also confer benefits in responding to certain biotic and abiotic stresses. This has led to the "cry for help" hypothesis, which is supported by the identification of plant genetic regulators integrating biotic/abiotic stress signaling and microbiota sculpting. Although diverse genetic mutants have been reported to affect microbiota composition, it has been challenging to confirm the causal link between specific microbiota changes and plant phenotypic outputs (e.g., fitness benefits) due to the complexity of microbial community composition. This limits the understanding of the relevance of plant-mediated microbiota changes. We reviewed the genetic bases of host-mediated reshaping of beneficial microbiota in response to biotic and abiotic stresses, and summarized the practical approaches linking microbiota changes and "functional outputs" in plants. Further understanding of the key regulators and pathways governing the assembly of stress-alleviating microbiota would benefit the design of crops that could dynamically enlist beneficial microbiota under conditions of stress.

bHLH11 inhibits bHLH IVc proteins by recruiting the TOPLESS/TOPLESS-RELATED corepressors

Iron (Fe) homeostasis is essential for plant growth and development. Many transcription factors (TFs) play pivotal roles in the maintenance of Fe homeostasis. bHLH11 is a negative TF that regulates Fe homeostasis. However, the underlying molecular mechanism remains elusive. Here, we generated two loss-of-function bhlh11 mutants in Arabidopsis (Arabidopsis thaliana), which display enhanced sensitivity to excess Fe, increased Fe accumulation, and elevated expression of Fe deficiency responsive genes. Levels of bHLH11 protein, localized in both the cytoplasm and nucleus, decreased in response to Fe deficiency. Co-expression assays indicated that bHLH IVc TFs (bHLH34, bHLH104, bHLH105, and bHLH115) facilitate the nuclear accumulation of bHLH11. Further analysis indicated that bHLH11 represses the transactivity of bHLH IVc TFs toward bHLH Ib genes (bHLH38, bHLH39, bHLH100, and bHLH101). The two ethylene response factor-associated amphiphilic repression motifs of bHLH11 provided the repression function by recruiting the TOPLESS/TOPLESS-RELATED (TPL/TPRs) corepressors. Correspondingly, the expression of Fe uptake genes increased in the tpr1 tpr4 tpl mutant. Moreover, genetic analysis revealed that bHLH11 has functions independent of FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR. This study provides insights into the complicated Fe homeostasis signaling network.

2021 update on ATP-binding cassette (ABC) transporters: how they meet the needs of plants

Recent developments in the field of ABC proteins including newly identified functions and regulatory mechanisms expand the understanding of how they function in the development and physiology of plants.