Coumarin accumulation and trafficking in Arabidopsis thaliana: a complex and dynamic process

Genes to specialized metabolites: accumulation of scopoletin, umbelliferone and their glycosides in natural populations of Arabidopsis thaliana

BACKGROUND

Scopoletin and umbelliferone belong to coumarins, which are plant specialized metabolites with potent and wide biological activities, the accumulation of which is induced by various environmental stresses. Coumarins have been detected in various plant species, including medicinal plants and the model organism Arabidopsis thaliana. In recent years, key role of coumarins in maintaining iron (Fe) homeostasis in plants has been demonstrated, as well as their significant impact on the rhizosphere microbiome through exudates secreted into the soil environment. Several mechanisms underlying these processes require clarification. Previously, we demonstrated that Arabidopsis is an excellent model for studying genetic variation and molecular basis of coumarin accumulation in plants.

RESULTS

Here, through targeted metabolic profiling and gene expression analysis, the gene-metabolite network of scopoletin and umbelliferone accumulation was examined in more detail in selected Arabidopsis accessions (Col-0, Est-1, Tsu-1) undergoing different culture conditions and characterized by variation in coumarin content. The highest accumulation of coumarins was detected in roots grown in vitro liquid culture. The expression of 10 phenylpropanoid genes (4CL1, 4CL2, 4CL3, CCoAOMT1, C3'H, HCT, F6'H1, F6'H2,CCR1 and CCR2) was assessed by qPCR in three genetic backgrounds, cultured in vitro and in soil, and in two types of tissues (leaves and roots). We not only detected the expected variability in gene expression and coumarin accumulation among Arabidopsis accessions, but also found interesting polymorphisms in the coding sequences of the selected genes through in silico analysis and resequencing.

CONCLUSIONS

To the best of our knowledge, this is the first study comparing accumulation of simple coumarins and expression of phenylpropanoid-related genes in Arabidopsis accessions grown in soil and in liquid cultures. The large variations we detected in the content of coumarins and gene expression are genetically determined, but also tissue and culture dependent. It is particularly important considering that growing plants in liquid media is a widely used technology that provides a large amount of root tissue suitable for metabolomics. Research on differential accumulation of coumarins and related gene expression will be useful in future studies aimed at better understanding the physiological role of coumarins in roots and the surrounding environments.

New molecular components that regulate the transcriptional hub in root hairs: coupling environmental signals with endogenous hormones to coordinate growth

Root hairs have become an important model system for studying plant growth, and in particular how plants modulate their growth in response to cell-intrinsic and environmental stimuli. In this review, we discuss recent advances in our understanding of the molecular mechanisms underlying the growth of Arabidopsis root hairs in the interface between responses to environmental cues (e.g. nutrients such as nitrates and phosphate, and microorganisms) and hormonal stimuli (e.g. auxin). Growth of root hairs is under the control of several transcription factors that are also under strong regulation at different levels. We highlight recent new discoveries along these transcriptional pathways that might have the potential to increase our capacity to enhance nutrient uptake by the roots in the context of abiotic stresses. We use the text-mining capacities of the PlantConnectome database to generate an up-to-date view of root hairs growth within these complex biological contexts.

Study on the Anti-Inflammatory Mechanism of Coumarins in Peucedanum decursivum Based on Spatial Metabolomics Combined with Network Pharmacology

Peucedanum decursivum (Miq.) Maxim (P. decursivum) is a traditional Chinese medicinal plant with pharmacological effects such as anti-inflammatory and anti-tumor effects, the root of which is widely used as medicine. Determining the spatial distribution and pharmacological mechanisms of metabolites is necessary when studying the effective substances of medicinal plants. As a means of obtaining spatial distribution information of metabolites, mass spectrometry imaging has high sensitivity and allows for molecule visualization. In this study, matrix-assisted laser desorption mass spectrometry (MALDI-TOF-MSI) and network pharmacology were used for the first time to visually study the spatial distribution and anti-inflammatory mechanism of coumarins, which are metabolites of P. decursivum, to determine their tissue localization and mechanism of action. A total of 27 coumarins were identified by MALDI-TOF-MSI, which mainly concentrated in the cortex, periderm, and phloem of the root of P. decursivum. Network pharmacology studies have identified key targets for the anti-inflammatory effect of P. decursivum, such as TNF, PTGS2, and PRAKA. GO enrichment and KEGG pathway analyses indicated that coumarins in P. decursivum mainly participated in biological processes such as inflammatory response, positive regulation of protein kinase B signaling, chemical carcinogenesis receptor activation, pathways in cancer, and other biological pathways. The molecular docking results indicated that there was good binding between components and targets. This study provides a basis for understanding the spatial distribution and anti-inflammatory mechanism of coumarins in P. decursivum.

Metal Transport Systems in Plants

Plants take up metals, including essential micronutrients [iron (Fe), copper (Cu), zinc (Zn), and manganese (Mn)] and the toxic heavy metal cadmium (Cd), from soil and accumulate these metals in their edible parts, which are direct and indirect intake sources for humans. Multiple transporters belonging to different families are required to transport a metal from the soil to different organs and tissues, but only a few of them have been fully functionally characterized. The transport systems (the transporters required for uptake, translocation, distribution, redistribution, and their regulation) differ with metals and plant species, depending on the physiological roles, requirements of each metal, and anatomies of different organs and tissues. To maintain metal homeostasis in response to spatiotemporal fluctuations of metals in soil, plants have developed sophisticated and tightly regulated mechanisms through the regulation of transporters at the transcriptional and/or posttranscriptional levels. The manipulation of some transporters has succeeded in generating crops rich in essential metals but low in Cd accumulation. A better understanding of metal transport systems will contribute to better and safer crop production.

Metal Homeostasis in Land Plants: A Perpetual Balancing Act Beyond the Fulfilment of Metalloproteome Cofactor Demands

One of life's decisive innovations was to harness the catalytic power of metals for cellular chemistry. With life's expansion, global atmospheric and biogeochemical cycles underwent dramatic changes. Although initially harmful, they permitted the evolution of multicellularity and the colonization of land. In land plants as primary producers, metal homeostasis faces heightened demands, in part because soil is a challenging environment for nutrient balancing. To avoid both nutrient metal limitation and metal toxicity, plants must maintain the homeostasis of metals within tighter limits than the homeostasis of other minerals. This review describes the present model of protein metalation and sketches its transfer from unicellular organisms to land plants as complex multicellular organisms. The inseparable connection between metal and redox homeostasis increasingly draws our attention to more general regulatory roles of metals. Mineral co-option, the use of nutrient or other metals for functions other than nutrition, is an emerging concept beyond that of nutritional immunity.

Comparative metabolic profiling of the mycelium and fermentation broth of Penicillium restrictum from Peucedanum praeruptorum rhizosphere

Microorganisms in the rhizosphere, particularly arbuscular mycorrhiza, have a broad symbiotic relationship with their host plants. One of the major fungi isolated from the rhizosphere of Peucedanum praeruptorum is Penicillium restrictum. The relationship between the metabolites of P. restrictum and the root exudates of P. praeruptorum is being investigated. The accumulation of metabolites in the mycelium and fermentation broth of P. restrictum was analysed over different fermentation periods. Non-targeted metabolomics was used to compare the differences in intracellular and extracellular metabolites over six periods. There were significant differences in the content and types of mycelial metabolites during the incubation. Marmesin, an important intermediate in the biosynthesis of coumarins, was found in the highest amount on the fourth day of incubation. The differential metabolites were screened to obtain 799 intracellular and 468 extracellular differential metabolites. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the highly enriched extracellular metabolic pathways were alanine, aspartate and glutamate metabolism, glyoxylate and dicarboxylate metabolism, and terpenoid backbone biosynthesis. In addition, the enrichment analysis associated with intracellular and extracellular ATP-binding cassette transporter proteins revealed that some ATP-binding cassette transporters may be involved in the transportation of certain amino acids and carbohydrates. Our results provide some theoretical basis for the regulatory mechanisms between the rhizosphere and the host plant and pave the way for the heterologous production of furanocoumarin.

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.

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.

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.

Stability of Coumarins and Determination of the Net Iron Oxidation State of Iron-Coumarin Complexes: Implications for Examining Plant Iron Acquisition Mechanisms

Coumarins are exuded into the soil environment by plant roots in response to iron (Fe) deficiency. Previous studies have shown that coumarins can increase the Fe solubility upon interaction with sparsely soluble Fe(III) (hydr)oxide. However, the chemical mechanisms of Fe(III) (hydr)oxide dissolution by coumarins remain unclear. The high redox instability of dissolved coumarins and the interference of coumarins in determining the Fe redox state hinder the quantitative and mechanistic investigation of coumarin-induced Fe mobilization. In this study, we investigated the oxidative stability of three coumarins that have been found in root exudates, esculetin, scopoletin, and fraxetin, over a broad pH range under oxic and anoxic conditions. Our results show that the oxidation of coumarins is irreversible under oxic conditions and that oxidative degradation rates increased with increasing pH under both oxic and anoxic conditions. However, the complexation of Fe protects coumarins from degradation in the circumneutral pH range even under oxic conditions. Furthermore, we observed that Ferrozine, which is commonly used for establishing Fe redox speciation, can facilitate the reduction of Fe(III) complexed by coumarins, even at circumneutral pH. Reduction rates increased with decreasing pH and were larger for fraxetin than for scopoletin and esculetin. Based on these observations, we optimized the Ferrozine method for determining the redox state of Fe complexed by coumarins. Understanding the stability of dissolved coumarins and using a precise analytical method to determine the redox state of Fe in the presence of coumarins are critical for investigating the mechanisms by which coumarins enhance the availability of Fe in the rhizosphere.

Anabolic metabolism of autotoxic substance coumarins in plants

Background

Autotoxicity is an intraspecific manifestation of allelopathy in plant species. The specialized metabolites and their derivatives that cause intraspecific allelopathic inhibition in the plant are known as autotoxic substances. Consequently, autotoxic substances production seriously affects the renewal and stability of ecological communities.

Methods

This article systematically summarizes the types of autotoxic substances present in different plants. They mainly include phenolic compounds, terpenoids, and nitrogenous organic compounds. Phenolic coumarins are the main autotoxic substances in many plants. Therefore, we also discuss differences in coumarin types and content among plant varieties, developmental stages, and tissue parts, as well as their mechanisms of autotoxicity. In addition, we review the metabolic pathways involved in coumarin biosynthesis, the key enzymes, genes, and transcription factors, as well as factors affecting coumarin biosynthesis.

Results

Coumarin biosynthesis involves three stages: (1) the formation of the coumarin nucleus; (2) acylation, hydroxylation, and cyclization; (3) structural modification. The key enzymes involved in the coumarin nuclear formation stage include PAL, C4H, 4CL, HCT, CAOMT, COSY, F6'H, and CCoAOMT1, and the key genes involved include BGA, CYP450 and MDR, among others. Ortho-hydroxylation is a key step in coumarin biosynthesis and PS, COSY and S8H are the key enzymes involved in this process. Finally, UGTs are responsible for the glycosylation modification of coumarins, and the MaUGT gene may therefore be involved in coumarin biosynthesis.

Conclusion

It is important to elucidate the autotoxicity and anabolic mechanisms of coumarins to create new germplasms that produce fewer autotoxic substances.

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.

Fraxetin alleviates BLM-induced idiopathic pulmonary fibrosis by inhibiting NCOA4-mediated epithelial cell ferroptosis

INTRODUCTION

Idiopathic pulmonary fibrosis (IPF) is a debilitating lung condition with few available treatments. The early driver of wound repair that contributes to IPF has been extensively identified as repetitive alveolar epithelial damage. According to recent reports, IPF is linked to ferroptosis, a unique type of cell death characterized by a fatal buildup of iron and lipid peroxidation.

OBJECTIVE AND METHOD

There is little information on epithelial cells that induce pulmonary fibrosis by going through ferroptosis. In this study, we used bleomycin (BLM) to examine the impact of ferroptosis on IPF in mouse lung epithelial cells (MLE-12).

RESULTS

We discovered that BLM increases ferroptosis in MLE-12. Additionally, we found that NCOA4 is overexpressed and plays a key role in the ferroptosis of epithelial cells throughout the IPF process. Using Molecular docking, we found that Fraxetin, a natural component extracted from Fraxinus rhynchophylla, formed a stable binding to NCOA4. In vitro investigations showed that Fraxetin administration greatly decreased ferroptosis and NCOA4 expression, which in turn lowered the release of inflammatory cytokines.

CONCLUSION

Fraxetin treatment significantly alleviated BLM-induced lung inflammation and fibrosis. Our findings imply that fraxetin possesses inhibitory roles in ferroptosis and can be a potential drug against IPF.

IMA peptides function in iron homeostasis and cadmium resistance

Iron (Fe), an essential micronutrient, participates in photosynthesis, respiration, and many other enzymatic reactions. Cadmium (Cd), by contrast, is a toxic element to virtually all living organisms. Both Fe deficiency and Cd toxicity severally impair crop growth and productivity, finally leading to human health issues. Understanding how plants control the uptake and homeostasis of Fe and combat Cd toxicity thus is mandatory to develop Fe-enriched but Cd-cleaned germplasms for human beings. Recent studies in Arabidopsis and rice have revealed that IRON MAN (IMA) peptides stand out as a key regulator to respond to Fe deficiency by competitively interacting with a ubiquitin E3 ligase, thus inhibiting the degradation of IVc subgroup bHLH transcription factors (TFs), mediated by 26 S proteasome. Elevated expression of IMA confers tolerance to Cd stress in both Arabidopsis and wheat by activating the iron deficiency response. Here, we discuss recent breakthroughs that IMA peptides function in the Fe-deficiency response to attain Fe homeostasis and combat Cd toxicity as a potential candidate for phytoremediation.

Hordeum vulgare differentiates its response to beneficial bacteria

BACKGROUND

In nature, beneficial bacteria triggering induced systemic resistance (ISR) may protect plants from potential diseases, reducing yield losses caused by diverse pathogens. However, little is known about how the host plant initially responds to different beneficial bacteria. To reveal the impact of different bacteria on barley (Hordeum vulgare), bacterial colonization patterns, gene expression, and composition of seed endophytes were explored.

RESULTS

This study used the soil-borne Ensifer meliloti, as well as Pantoea sp. and Pseudomonas sp. isolated from barley seeds, individually. The results demonstrated that those bacteria persisted in the rhizosphere but with different colonization patterns. Although root-leaf translocation was not observed, all three bacteria induced systemic resistance (ISR) against foliar fungal pathogens. Transcriptome analysis revealed that ion- and stress-related genes were regulated in plants that first encountered bacteria. Iron homeostasis and heat stress responses were involved in the response to E. meliloti and Pantoea sp., even if the iron content was not altered. Heat shock protein-encoding genes responded to inoculation with Pantoea sp. and Pseudomonas sp. Furthermore, bacterial inoculation affected the composition of seed endophytes. Investigation of the following generation indicated that the enhanced resistance was not heritable.

CONCLUSIONS

Here, using barley as a model, we highlighted different responses to three different beneficial bacteria as well as the influence of soil-borne Ensifer meliloti on the seed microbiome. In total, these results can help to understand the interaction between ISR-triggering bacteria and a crop plant, which is essential for the application of biological agents in sustainable agriculture.

Iron-dependent regulation of leaf senescence: a key role for the H2B histone variant HTB4

This article is a Commentary on Yang et al. (2023), 240: 694–709.

Mass spectrometry imaging and single-cell transcriptional profiling reveal the tissue-specific regulation of bioactive ingredient biosynthesis in Taxus leaves

Taxus leaves provide the raw industrial materials for taxol, a natural antineoplastic drug widely used in the treatment of various cancers. However, the precise distribution, biosynthesis, and transcriptional regulation of taxoids and other active components in Taxus leaves remain unknown. Matrix-assisted laser desorption/ionization-mass spectrometry imaging analysis was used to visualize various secondary metabolites in leaf sections of Taxus mairei, confirming the tissue-specific accumulation of different active metabolites. Single-cell sequencing was used to produce expression profiles of 8846 cells, with a median of 2352 genes per cell. Based on a series of cluster-specific markers, cells were grouped into 15 clusters, suggesting a high degree of cell heterogeneity in T. mairei leaves. Our data were used to create the first Taxus leaf metabolic single-cell atlas and to reveal spatial and temporal expression patterns of several secondary metabolic pathways. According to the cell-type annotation, most taxol biosynthesis genes are expressed mainly in leaf mesophyll cells; phenolic acid and flavonoid biosynthesis genes are highly expressed in leaf epidermal cells (including the stomatal complex and guard cells); and terpenoid and steroid biosynthesis genes are expressed specifically in leaf mesophyll cells. A number of novel and cell-specific transcription factors involved in secondary metabolite biosynthesis were identified, including MYB17, WRKY12, WRKY31, ERF13, GT_2, and bHLH46. Our research establishes the transcriptional landscape of major cell types in T. mairei leaves at a single-cell resolution and provides valuable resources for studying the basic principles of cell-type-specific regulation of secondary metabolism.

Iron transport mechanisms and their evolution focusing on chloroplasts

Iron (Fe) is an essential element for photosynthetic organisms, required for several vital biological functions. Photosynthesis, which takes place in the chloroplasts of higher plants, is the major Fe consumer. Although the components of the root Fe uptake system in dicotyledonous and monocotyledonous plants have been extensively studied, the Fe transport mechanisms of chloroplasts in these two groups of plants have received little attention. This review focuses on the comparative analysis of Fe transport processes in the evolutionary ancestors of chloroplasts (cyanobacteria) with the processes in embryophytes and green algae (Viridiplantae). The aim is to summarize how chloroplasts are integrated into cellular Fe homeostasis and how Fe transporters and Fe transport mechanisms have been modified by evolution.

Multi-omics reveal key enzymes involved in the formation of phenylpropanoid glucosides in Artemisia annua

Although mainly known for producing artemisinin, Artemisia annua is enriched in phenylpropanoid glucosides (PGs) with significant bioactivities. However, the biosynthesis of A. annua PGs is insufficiently investigated. Different A. annua ecotypes from distinct growing environments accumulate varying amounts of metabolites, including artemisinin and PGs such as scopolin. UDP-glucose:phenylpropanoid glucosyltransferases (UGTs) transfers glucose from UDP-glucose in PG biosynthesis. Here, we found that the low-artemisinin ecotype GS produces a higher amount of scopolin, compared to the high-artemisinin ecotype HN. By combining transcriptome and proteome analyses, we selected 28 candidate AaUGTs from 177 annotated AaUGTs. Using AlphaFold structural prediction and molecular docking, we determined the binding affinities of 16 AaUGTs. Seven of the AaUGTs enzymatically glycosylated phenylpropanoids. AaUGT25 converted scopoletin to scopolin and esculetin to esculin. The lack of accumulation of esculin in the leaf and the high catalytic efficiency of AaUGT25 on esculetin suggest that esculetin is methylated to scopoletin, the precursor of scopolin. We also discovered that AaOMT1, a previously uncharacterized O-methyltransferase, converts esculetin to scopoletin, suggesting an alternative route for producing scopoletin, which contributes to the high-level accumulation of scopolin in A. annua leaves. AaUGT1 and AaUGT25 responded to induction of stress-related phytohormones, implying the involvement of PGs in stress responses.

Cell-type-specific transcriptomics reveals that root hairs and endodermal barriers play important roles in beneficial plant-rhizobacterium interactions

Growth- and health-promoting bacteria can boost crop productivity in a sustainable way. Pseudomonas simiae WCS417 is such a bacterium that efficiently colonizes roots, modifies the architecture of the root system to increase its size, and induces systemic resistance to make plants more resistant to pests and pathogens. Our previous work suggested that WCS417-induced phenotypes are controlled by root cell-type-specific mechanisms. However, it remains unclear how WCS417 affects these mechanisms. In this study, we transcriptionally profiled five Arabidopsis thaliana root cell types following WCS417 colonization. We found that the cortex and endodermis have the most differentially expressed genes, even though they are not in direct contact with this epiphytic bacterium. Many of these genes are associated with reduced cell wall biogenesis, and mutant analysis suggests that this downregulation facilitates WCS417-driven root architectural changes. Furthermore, we observed elevated expression of suberin biosynthesis genes and increased deposition of suberin in the endodermis of WCS417-colonized roots. Using an endodermal barrier mutant, we showed the importance of endodermal barrier integrity for optimal plant-beneficial bacterium association. Comparison of the transcriptome profiles in the two epidermal cell types that are in direct contact with WCS417-trichoblasts that form root hairs and atrichoblasts that do not-implies a difference in potential for defense gene activation. While both cell types respond to WCS417, trichoblasts displayed both higher basal and WCS417-dependent activation of defense-related genes compared with atrichoblasts. This suggests that root hairs may activate root immunity, a hypothesis that is supported by differential immune responses in root hair mutants. Taken together, these results highlight the strength of cell-type-specific transcriptional profiling to uncover "masked" biological mechanisms underlying beneficial plant-microbe associations.

Research progress on iron absorption, transport, and molecular regulation strategy in plants

Iron is a trace element essential for normal plant life activities and is involved in various metabolic pathways such as chlorophyll synthesis, photosynthesis, and respiration. Although iron is highly abundant in the earth's crust, the amount that can be absorbed and utilized by plants is very low. Therefore, plants have developed a series of systems for absorption, transport, and utilization in the course of long-term evolution. This review focuses on the findings of current studies of the Fe²⁺ absorption mechanism I, Fe³⁺ chelate absorption mechanism II and plant-microbial interaction iron absorption mechanism, particularly effective measures for artificially regulating plant iron absorption and transportation to promote plant growth and development. According to the available literature, the beneficial effects of using microbial fertilizers as iron fertilizers are promising but further evidence of the interaction mechanism between microorganisms and plants is required.

Regulation of the iron-deficiency response by IMA/FEP peptide

Iron (Fe) is an essential micronutrient for plant growth and development, participating in many significant biological processes including photosynthesis, respiration, and nitrogen fixation. Although abundant in the earth's crust, most Fe is oxidized and difficult for plants to absorb under aerobic and alkaline pH conditions. Plants, therefore, have evolved complex means to optimize their Fe-acquisition efficiency. In the past two decades, regulatory networks of transcription factors and ubiquitin ligases have proven to be essential for plant Fe uptake and translocation. Recent studies in Arabidopsis thaliana (Arabidopsis) suggest that in addition to the transcriptional network, IRON MAN/FE-UPTAKE-INDUCING PEPTIDE (IMA/FEP) peptide interacts with a ubiquitin ligase, BRUTUS (BTS)/BTS-LIKE (BTSL). Under Fe-deficient conditions, IMA/FEP peptides compete with IVc subgroup bHLH transcription factors (TFs) to interact with BTS/BTSL. The resulting complex inhibits the degradation of these TFs by BTS/BTSL, which is important for maintaining the Fe-deficiency response in roots. Furthermore, IMA/FEP peptides control systemic Fe signaling. By organ-to-organ communication in Arabidopsis, Fe deficiency in one part of a root drives the upregulation of a high-affinity Fe-uptake system in other root regions surrounded by sufficient levels of Fe. IMA/FEP peptides regulate this compensatory response through Fe-deficiency-triggered organ-to-organ communication. This mini-review summarizes recent advances in understanding how IMA/FEP peptides function in the intracellular signaling of the Fe-deficiency response and systemic Fe signaling to regulate Fe acquisition.

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.

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.

Arabidopsis Micro-grafting to Study the Systemic Signaling of Nutrient Status

Grafting enables the study of systemic signals that plants use to maintain their homeostasis at the level of the whole organism. Several protocols of Arabidopsis grafting have been published over the years. These methods are limited because they either affect the overall behavior of the plant, or their throughput is low. The method presented here is based on grafting 3- to 4-days-old seedlings directly on an agar plate, without the use of hormone or collar, and can produce consistently over a hundred grafted plants per day and operator.

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.

Gossypol and related compounds are produced and accumulate in the aboveground parts of the cotton plant, independent of roots as the source

Use of Ultra-low gossypol cottonseed event as a scion in a graft combination confirmed that roots are not a source of terpenoids in the aboveground parts of a cotton plant. Gossypol and related terpenoids, derived from the same basic biosynthetic pathway, are present in the numerous lysigenous glands in the aboveground parts of a cotton plant. Roots, with sparse presence of such glands, do produce significant amount of gossypol and a different set of terpenoids. These compounds serve a defensive function against various pests and pathogens. This investigation was undertaken to examine whether gossypol produced in the roots can replenish the gossypol content of the cottonseed-glands that are largely devoid of this terpenoid in a genetically engineered event. Graft unions between a scion derived from the RNAi-based, Ultra-low gossypol cottonseed (ULGCS) event, TAM66274, and a rootstock derived from wild-type parental genotype, Coker 312 (Coker), were compared with various other grafts that served as controls. The results showed that the seeds developing within the scion of test grafts (ULGCS/Coker) continued to maintain the ultra-low gossypol levels found in the TAM66274 seeds. Molecular analyses confirmed that while the key gene involved in gland development showed normal activity in the developing embryos in the scion, two genes encoding the enzymes involved in gossypol biosynthesis were suppressed. Thus, the gene expression data confirmed the results obtained from biochemical measurements and collectively demonstrated that roots are not a source of gossypol for the aboveground parts of the cotton plant. These findings, combined with the results from previous investigations, support the assertion that gossypol and related terpenoids are produced in a highly localized manner in various organs of the cotton plant and are retained therein.

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.

FE UPTAKE-INDUCING PEPTIDE1 maintains Fe translocation by controlling Fe deficiency response genes in the vascular tissue of Arabidopsis

FE UPTAKE-INDUCING PEPTIDE1 (FEP1), also named IRON MAN3 (IMA3) is a short peptide involved in the iron deficiency response in Arabidopsis thaliana. Recent studies uncovered its molecular function, but its physiological function in the systemic Fe response is not fully understood. To explore the physiological function of FEP1 in iron homoeostasis, we performed a transcriptome analysis using the FEP1 loss-of-function mutant fep1-1 and a transgenic line with oestrogen-inducible expression of FEP1. We determined that FEP1 specifically regulates several iron deficiency-responsive genes, indicating that FEP1 participates in iron translocation rather than iron uptake in roots. The iron concentration in xylem sap under iron-deficient conditions was lower in the fep1-1 mutant and higher in FEP1-induced transgenic plants compared with the wild type (WT). Perls staining revealed a greater accumulation of iron in the cortex of fep1-1 roots than in the WT root cortex, although total iron levels in roots were comparable in the two genotypes. Moreover, the fep1-1 mutation partially suppressed the iron overaccumulation phenotype in the leaves of the oligopeptide transporter3-2 (opt3-2) mutant. These data suggest that FEP1 plays a pivotal role in iron movement and in maintaining the iron quota in vascular tissues in Arabidopsis.

Carbonate-Induced Chemical Reductants Are Responsible for Iron Acquisition in Strategy I Wild Herbaceous Plants Native to Calcareous Grasslands

Significant progress has been made in understanding Strategy I iron (Fe) acquisition using crop/model plants under controlled conditions in laboratories. However, plant species native to calcareous soils may have evolved unique strategies for adaptation to high carbonate/pH-induced Fe deficiency. Until now, little information is available on the Fe acquisition mechanisms in these plants. Here, we explored the Fe acquisition mechanisms in wild dicot species native to calcareous grasslands, by monitoring the Fe nutrition-related rhizosphere processes in field and greenhouse conditions. Most of these wild species displayed comparable shoot Fe concentration to those of crops, and some dicots actually accumulated very high shoot Fe. However, these species did not exhibit ferric reductase oxidase (FRO)-dependent Strategy I responses to Fe deficiency, including visual rhizosphere acidification and increased Fe3+ reduction. In contrast, chemical reductants exuded by roots of dicots were responsible for Fe3+ reduction in these wild plants. These features were not observed in the FRO-dependent Strategy I crop plant cucumber. Neither leaf chlorophyll nor shoot/root Fe was depressed by 10% CaCO3 application in all the examined wild species. Furthermore, their root exudation was significantly activated by CaCO3, leading to an increased Fe3+ reduction. We show that chemical reductant-mediated Fe3+ reduction occurs preferentially in these wild dicots and that these mechanisms are not sensitive to high soil carbonate/pH. Our findings support that Fe acquisition in Strategy I wild plants native to calcareous soils is substantially different from the enzyme-dependent system of Strategy I plants.

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.

Retrieving the in vivo Scopoletin Fluorescence Excitation Band Allows the Non-invasive Investigation of the Plant-Pathogen Early Events in Tobacco Leaves

In this study, we developed and applied a new spectroscopic fluorescence method for the in vivo detection of the early events in the interaction between tobacco (Nicotiana tabacum L.) plants and pathogenic bacteria. The leaf disks were infiltrated with a bacterial suspension in sterile physiological solution (SPS), or with SPS alone as control. The virulent Pseudomonas syringae pv. tabaci strain ATCC 11528, its non-pathogenic ΔhrpA mutant, and the avirulent P. syringae pv. tomato strain DC3000 were used. At different post-infiltration time-points, the in vivo fluorescence spectra on leaf disks were acquired by a fiber bundle-spectrofluorimeter. The excitation spectra of the leaf blue emission at 460 nm, which is mainly due to the accumulation of coumarins following a bacterial infiltration, were processed by using a two-bands Gaussian fitting that enabled us to isolate the scopoletin (SCT) contribution. The pH-dependent fluorescence of SCT and scopolin (SCL), as determined by in vitro data and their intracellular localization, as determined by confocal microscopy, suggested the use of the longer wavelength excitation band at 385 nm of 460 nm emission (F385_460) to follow the metabolic evolution of SCT during the plant-bacteria interaction. It was found to be directly correlated (R 2 = 0.84) to the leaf SCT content, but not to that of SCL, determined by HPLC analysis. The technique applied to the time-course monitoring of the bacteria-plant interaction clearly showed that the amount and the timing of SCT accumulation, estimated by F385_460, was correlated with the resistance to the pathogen. As expected, this host defense response was delayed after P. syringae pv. tabaci ATCC 11528 infiltration, in comparison to P. syringae pv. tomato DC3000. Furthermore, no significant increase of F385_460 (SCT) was observed when using the non-pathogenic ΔhrpA mutant of P. syringae pv. tabaci ATCC 11528, which lacks a functional Type Three Secretion System (TTSS). Our study showed the reliability of the developed fluorimetric method for a rapid and non-invasive monitoring of bacteria-induced first events related to the metabolite-based defense response in tobacco leaves. This technique could allow a fast selection of pathogen-resistant cultivars, as well as the on-site early diagnosis of tobacco plant diseases by using suitable fluorescence sensors.

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.

Grafting: a potential method to reveal the differential accumulation mechanism of secondary metabolites

Plant secondary metabolites make a great contribution to the agricultural and pharmaceutical industries. Their accumulation is determined by the integrated transport of target compounds and their biosynthesis-related RNA, protein, or DNA. However, it is hard to track the movement of these biomolecules in vivo. Grafting may be an ideal method to solve this problem. The differences in genetic and metabolic backgrounds between rootstock and scion, coupled with multiple omics approaches and other molecular tools, make it feasible to determine the movement of target compounds, RNAs, proteins, and DNAs. In this review, we will introduce methods of using the grafting technique, together with molecular biological tools, to reveal the differential accumulation mechanism of plant secondary metabolites at different levels. Details of the case of the transport of one diterpene alkaloid, fuziline, will be further illustrated to clarify how the specific accumulation model is shaped with the help of grafting and multiple molecular biological tools.

How Plants Recalibrate Cellular Iron Homeostasis

Insufficient iron supply poses severe constraints on plants, restricting species with inefficient iron uptake mechanisms from habitats with low iron availability and causing yield losses in agricultural ecosystems. Iron deficiency also poses a severe threat on human health. Anemia resulting from insufficient iron intake is affecting one of four people in the world. It is, therefore, imperative to understand the mechanisms by which plants acquire iron against a huge soil-cell gradient and how iron is distributed within the plant to develop strategies that increase its concentration in edible plant parts. Research into the processes that are employed by plants to adjust cellular iron homeostasis revealed an astonishingly complex puzzle of signaling nodes and circuits, which are intertwined with the perception and communication of other environmental cues such as pathogens, light, nutrient availability and edaphic factors such as pH. In a recent Spotlight issue in this journal, a collection of review articles summarized the state-of-the-art in plant iron research, covering the most active and, debatably, most important topics in this field. Here, we highlight breakthroughs that were reported after the publication date of this review collection, focusing on exciting and potentially influential studies that have changed our understanding of plant iron nutrition.

Solving the puzzle of Fe homeostasis by integrating molecular, mathematical, and societal models

To ensure optimal utilization and bioavailability, iron uptake, transport, subcellular localization, and assimilation are tightly regulated in plants. Herein, we examine recent advances in our understanding of cellular responses to Fe deficiency. We then use intracellular mechanisms of Fe homeostasis to discuss how formalizing cell biology knowledge via a mathematical model can advance discovery even when quantitative data is limited. Using simulation-based inference to identify plausible systems mechanisms that conform to known emergent phenotypes can yield novel, testable hypotheses to guide targeted experiments. However, this approach relies on the accurate encoding of domain-expert knowledge in exploratory mathematical models. We argue that this would be facilitated by fostering more "systems thinking" life scientists and that diversifying your research team may be a practical path to achieve that goal.

IRONMAN tunes responses to iron deficiency in concert with environmental pH

Iron (Fe) is an essential mineral element that governs the composition of natural plant communities and limits crop yield in agricultural ecosystems due to its extremely low availability in most soils, particularly at alkaline pH. To extract sufficient Fe from the soil under such conditions, some plants, including Arabidopsis (Arabidopsis thaliana), secrete Fe-mobilizing phenylpropanoids, which mobilize sparingly soluble Fe hydroxides by reduction and chelation. We show here that ectopic expression of the peptides IRONMAN (IMA1) and IMA2 improves growth on calcareous soil by inducing biosynthesis and secretion of the catecholic coumarin 7,8-dihydroxy-6-methoxycoumarin (fraxetin) via increased expression of MYB72 and SCOPOLETIN 8-HYDROXYLASE, a response that is strictly dependent on elevated environmental pH (pHe). By contrast, transcription of the cytochrome P450 family protein CYP82C4, catalyzing the subsequent hydroxylation of fraxetin to sideretin, which forms less stable complexes with iron, was strongly repressed under such conditions. We concluded that IMA peptides regulate processes supporting Fe uptake at both acidic and elevated pH by controlling gene expression upstream of or in concert with a putative pHe signal, adapting the plant to prevailing edaphic conditions. This regulatory pattern confers tolerance to calcareous soils by extending the pH range in which Fe can be efficiently absorbed from the soil. Our results further suggest that pHe calibrates the activities of components of the Fe deficiency response, accentuating processes that are most efficient under the prevailing conditions. Altering the expression of IMA peptides provides a route for generating plants adapted to calcareous soils.

A quick journey into the diversity of iron uptake strategies in photosynthetic organisms

Iron (Fe) is involved in multiple processes that contribute to the maintenance of the cellular homeostasis of all living beings. In photosynthetic organisms, Fe is notably required for photosynthesis. Although iron is generally abundant in the environment, it is frequently poorly bioavailable. This review focuses on the molecular strategies that photosynthetic organisms have evolved to optimize iron acquisition, using Arabidopsis thaliana, rice (Oryza sativa), and some unicellular algae as models. Non-graminaceous plants, including Arabidopsis, take up iron from the soil by an acidification-reduction-transport process (strategy I) requiring specific proteins that were recently shown to associate in a dedicated complex. On the other hand, graminaceous plants, such as rice, use the so-called strategy II to acquire iron, which relies on the uptake of Fe³⁺ chelated by phytosiderophores that are secreted by the plant into the rhizosphere. However, apart these main strategies, accessory mechanisms contribute to robust iron uptake in both Arabidopsis and rice. Unicellular algae combine reductive and non-reductive mechanisms for iron uptake and present important specificities compared to land plants. Since the majority of the molecular actors required for iron acquisition in algae are not conserved in land plants, questions arise about the evolution of the Fe uptake processes upon land colonization.

Mining Fiskeby III and Mandarin (Ottawa) Expression Profiles to Understand Iron Stress Tolerant Responses in Soybean

The soybean (Glycine max L. merr) genotype Fiskeby III is highly resistant to a multitude of abiotic stresses, including iron deficiency, incurring only mild yield loss during stress conditions. Conversely, Mandarin (Ottawa) is highly susceptible to disease and suffers severe phenotypic damage and yield loss when exposed to abiotic stresses such as iron deficiency, a major challenge to soybean production in the northern Midwestern United States. Using RNA-seq, we characterize the transcriptional response to iron deficiency in both Fiskeby III and Mandarin (Ottawa) to better understand abiotic stress tolerance. Previous work by our group identified a quantitative trait locus (QTL) on chromosome 5 associated with Fiskeby III iron efficiency, indicating Fiskeby III utilizes iron deficiency stress mechanisms not previously characterized in soybean. We targeted 10 of the potential candidate genes in the Williams 82 genome sequence associated with the QTL using virus-induced gene silencing. Coupling virus-induced gene silencing with RNA-seq, we identified a single high priority candidate gene with a significant impact on iron deficiency response pathways. Characterization of the Fiskeby III responses to iron stress and the genes underlying the chromosome 5 QTL provides novel targets for improved abiotic stress tolerance in soybean.

Suberin plasticity to developmental and exogenous cues is regulated by a set of MYB transcription factors

Suberin is a hydrophobic biopolymer that can be deposited at the periphery of cells, forming protective barriers against biotic and abiotic stress. In roots, suberin forms lamellae at the periphery of endodermal cells where it plays crucial roles in the control of water and mineral transport. Suberin formation is highly regulated by developmental and environmental cues. However, the mechanisms controlling its spatiotemporal regulation are poorly understood. Here, we show that endodermal suberin is regulated independently by developmental and exogenous signals to fine-tune suberin deposition in roots. We found a set of four MYB transcription factors (MYB41, MYB53, MYB92, and MYB93), each of which is individually regulated by these two signals and is sufficient to promote endodermal suberin. Mutation of these four transcription factors simultaneously through genome editing leads to a dramatic reduction in suberin formation in response to both developmental and environmental signals. Most suberin mutants analyzed at physiological levels are also affected in another endodermal barrier made of lignin (Casparian strips) through a compensatory mechanism. Through the functional analysis of these four MYBs, we generated plants allowing unbiased investigation of endodermal suberin function, without accounting for confounding effects due to Casparian strip defects, and were able to unravel specific roles of suberin in nutrient homeostasis.

Unravelling the Puzzle of Anthranoid Metabolism in Living Plant Cells Using Spectral Imaging Coupled to Mass Spectrometry

Vismione H (VH) is a fluorescent prenylated anthranoid produced by plants from the Hypericaceae family, with antiprotozoal activities against malaria and leishmaniosis. Little is known about its biosynthesis and metabolism in plants or its mode of action against parasites. When VH is isolated from Psorospermum glaberrimum, it is rapidly converted into madagascine anthrone and anthraquinone, which are characterized by markedly different fluorescent properties. To locate the fluorescence of VH in living plant cells and discriminate it from that of the other metabolites, an original strategy combining spectral imaging (SImaging), confocal microscopy, and non-targeted metabolomics using mass spectrometry, was developed. Besides VH, structurally related molecules including madagascine (Mad), emodin (Emo), quinizarin (Qui), as well as lapachol (Lap) and fraxetin (Fra) were analyzed. This strategy readily allowed a spatiotemporal characterization and discrimination of spectral fingerprints from anthranoid-derived metabolites and related complexes with cations and proteins. In addition, our study validates the ability of plant cells to metabolize VH into madagascine anthrone, anthraquinones and unexpected metabolites. These results pave the way for new hypotheses on anthranoid metabolism in plants.

Coumarin Interferes with Polar Auxin Transport Altering Microtubule Cortical Array Organization in Arabidopsis thaliana (L.) Heynh. Root Apical Meristem

Coumarin is a phytotoxic natural compound able to affect plant growth and development. Previous studies have demonstrated that this molecule at low concentrations (100 µM) can reduce primary root growth and stimulate lateral root formation, suggesting an auxin-like activity. In the present study, we evaluated coumarin’s effects (used at lateral root-stimulating concentrations) on the root apical meristem and polar auxin transport to identify its potential mode of action through a confocal microscopy approach. To achieve this goal, we used several Arabidopsis thaliana GFP transgenic lines (for polar auxin transport evaluation), immunolabeling techniques (for imaging cortical microtubules), and GC-MS analysis (for auxin quantification). The results highlighted that coumarin induced cyclin B accumulation, which altered the microtubule cortical array organization and, consequently, the root apical meristem architecture. Such alterations reduced the basipetal transport of auxin to the apical root apical meristem, inducing its accumulation in the maturation zone and stimulating lateral root formation.

Adaptation of Arabidopsis halleri to extreme metal pollution through limited metal accumulation involves changes in cell wall composition and metal homeostasis

Metallophytes constitute powerful models for the study of metal homeostasis, adaptation to extreme environments and the evolution of naturally selected traits. Arabidopsis halleri is a pseudometallophyte which shows constitutive zinc/cadmium (Zn/Cd) tolerance and Zn hyperaccumulation but high intraspecific variability in Cd accumulation. To examine the molecular basis of the variation in metal tolerance and accumulation, ionome, transcriptome and cell wall glycan array profiles were compared in two genetically close A. halleri populations from metalliferous and nonmetalliferous sites in Northern Italy. The metallicolous population displayed increased tolerance to and reduced hyperaccumulation of Zn, and limited accumulation of Cd, as well as altered metal homeostasis, compared to the nonmetallicolous population. This correlated well with the differential expression of transporter genes involved in trace metal entry and in Cd/Zn vacuolar sequestration in roots. Many cell wall-related genes were also more highly expressed in roots of the metallicolous population. Glycan array and histological staining analyses demonstrated that there were major differences between the two populations in terms of the accumulation of specific root pectin and hemicellulose epitopes. Our results support the idea that both specific cell wall components and regulation of transporter genes play a role in limiting accumulation of metals in A. halleri at contaminated sites.

Identification and Quantification of Coumarins by UHPLC-MS in Arabidopsis thaliana Natural Populations

Coumarins are phytochemicals occurring in the plant kingdom, which biosynthesis is induced under various stress factors. They belong to the wide class of specialized metabolites well known for their beneficial properties. Due to their high and wide biological activities, coumarins are important not only for the survival of plants in changing environmental conditions, but are of great importance in the pharmaceutical industry and are an active source for drug development. The identification of coumarins from natural sources has been reported for different plant species including a model plant Arabidopsis thaliana. In our previous work, we demonstrated a presence of naturally occurring intraspecies variation in the concentrations of scopoletin and its glycoside, scopolin, the major coumarins accumulating in Arabidopsis roots. Here, we expanded this work by examining a larger group of 28 Arabidopsis natural populations (called accessions) and by extracting and analysing coumarins from two different types of tissues-roots and leaves. In the current work, by quantifying the coumarin content in plant extracts with ultra-high-performance liquid chromatography coupled with a mass spectrometry analysis (UHPLC-MS), we detected a significant natural variation in the content of simple coumarins like scopoletin, umbelliferone and esculetin together with their glycosides: scopolin, skimmin and esculin, respectively. Increasing our knowledge of coumarin accumulation in Arabidopsis natural populations, might be beneficial for the future discovery of physiological mechanisms of action of various alleles involved in their biosynthesis. A better understanding of biosynthetic pathways of biologically active compounds is the prerequisite step in undertaking a metabolic engineering research.