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

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.

Transcriptomic Changes in Internode Explants of Stinging Nettle during Callogenesis

Callogenesis, the process during which explants derived from differentiated plant tissues are subjected to a trans-differentiation step characterized by the proliferation of a mass of cells, is fundamental to indirect organogenesis and the establishment of cell suspension cultures. Therefore, understanding how callogenesis takes place is helpful to plant tissue culture, as well as to plant biotechnology and bioprocess engineering. The common herbaceous plant stinging nettle (Urtica dioica L.) is a species producing cellulosic fibres (the bast fibres) and a whole array of phytochemicals for pharmacological, nutraceutical and cosmeceutical use. Thus, it is of interest as a potential multi-purpose plant. In this study, callogenesis in internode explants of a nettle fibre clone (clone 13) was studied using RNA-Seq to understand which gene ontologies predominate at different time points. Callogenesis was induced with the plant growth regulators α-napthaleneacetic acid (NAA) and 6-benzyl aminopurine (BAP) after having determined their optimal concentrations. The process was studied over a period of 34 days, a time point at which a well-visible callus mass developed on the explants. The bioinformatic analysis of the transcriptomic dataset revealed specific gene ontologies characterizing each of the four time points investigated (0, 1, 10 and 34 days). The results show that, while the advanced stage of callogenesis is characterized by the iron deficiency response triggered by the high levels of reactive oxygen species accumulated by the proliferating cell mass, the intermediate and early phases are dominated by ontologies related to the immune response and cell wall loosening, respectively.

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.

Pathogens pulling the strings: Effectors manipulating salicylic acid and phenylpropanoid biosynthesis in plants

During evolution, plants have developed sophisticated ways to cope with different biotic and abiotic stresses. Phytohormones and secondary metabolites are known to play pivotal roles in defence responses against invading pathogens. One of the key hormones involved in plant immunity is salicylic acid (SA), of which the role in plant defence is well established and documented. Plants produce an array of secondary metabolites categorized in different classes, with the phenylpropanoids as major players in plant immunity. Both SA and phenylpropanoids are needed for an effective immune response by the plant. To successfully infect the host, pathogens secrete proteins, called effectors, into the plant tissue to lower defence. Secreted effectors can interfere with several metabolic or signalling pathways in the host to facilitate infection. In this review, we will focus on the different strategies pathogens have developed to affect the levels of SA and phenylpropanoids to increase plant susceptibility.

Zinc uptake and HMA4 activity are required for micro- and macroelement balance in tobacco (Nicotiana tabacum)

The pleiotropic effects of zinc deficiency on ion homeostasis have already been described in several plants. Tobacco (Nicotiana tabacum) heavy metal ATPases HMA4.1 and HMA4.2 are involved in zinc and cadmium root-to-shoot translocation. In previous research, we have shown that N. tabacum HMA4 RNAi plants and HMA4 double-nonsense mutants exhibit strongly reduced zinc and cadmium levels in leaves as well as stunted growth. In this study, the ionome and transcriptome of these lines were investigated to better characterize the effect of reduced zinc levels and to understand the impaired growth phenotype. We found that, under standard greenhouse fertilization rates, these lines accumulated up to 4- to 6-fold more phosphorus, iron, manganese, and copper than their respective controls. Under field conditions, HMA4 double-mutant plants also exhibited similar accumulation phenotypes, albeit to a lower extent. In both HMA4 RNAi plants and HMA4 mutants, transcription analysis showed a local zinc-deficiency response in leaves as well as an FIT1-mediated iron-deficiency response in roots, likely contributing to iron and manganese uptake at the root level. A phosphate-starvation response involving HHO2 was also observed in HMA4-impaired plant leaves. The high level of phosphorus observed in HMA4-impaired plants is correlated with leaf swelling and necrosis. The upregulation of aquaporin genes is in line with cellular water influx and the observed leaf swelling phenotype. These results highlight the involvement of HMA4 in zinc homeostasis and related regulatory processes that balance the micro- and macroelements in above-ground organs.

Plasticity, exudation and microbiome-association of the root system of Pellitory-of-the-wall plants grown in environments impaired in iron availability

The investigation of the adaptive strategies of wild plant species to extreme environments is a challenging issue, which favors the identification of new traits for plant resilience. We investigated different traits which characterize the root-soil interaction of Parietaria judaica, a wild plant species commonly known as "Pellitory-of-the-wall". P. judaica adopts the acidification-reduction strategy (Strategy I) for iron (Fe) acquisition from soil, and it can complete its life cycle in highly calcareous environments without any symptoms of chlorosis. In a field-to-lab approach, the microbiome associated with P. judaica roots was analyzed in spontaneous plants harvested from an urban environment consisting in an extremely calcareous habitat. Also, the phenolics and carboxylates content and root plasticity and exudation were analyzed in P. judaica plants grown under three different controlled conditions mimicking the effect of calcareous environments on Fe availability: results show that P. judaica differentially modulates root plasticity under different Fe availability-impaired conditions, and that it induces, to a high extent, the exudation of caffeoylquinic acid derivatives under calcareous conditions, positively impacting Fe solubility.

Plant Secondary Metabolite Transporters: Diversity, Functionality, and Their Modulation

Secondary metabolites (SMs) play crucial roles in the vital functioning of plants such as growth, development, defense, and survival via their transportation and accumulation at the required site. However, unlike primary metabolites, the transport mechanisms of SMs are not yet well explored. There exists a huge gap between the abundant presence of SM transporters, their identification, and functional characterization. A better understanding of plant SM transporters will surely be a step forward to fulfill the steeply increasing demand for bioactive compounds for the formulation of herbal medicines. Thus, the engineering of transporters by modulating their expression is emerging as the most viable option to achieve the long-term goal of systemic metabolic engineering for enhanced metabolite production at minimum cost. In this review article, we are updating the understanding of recent advancements in the field of plant SM transporters, particularly those discovered in the past two decades. Herein, we provide notable insights about various types of fully or partially characterized transporters from the ABC, MATE, PUP, and NPF families including their diverse functionalities, structural information, potential approaches for their identification and characterization, several regulatory parameters, and their modulation. A novel perspective to the concept of "Transporter Engineering" has also been unveiled by highlighting its potential applications particularly in plant stress (biotic and abiotic) tolerance, SM accumulation, and removal of anti-nutritional compounds, which will be of great value for the crop improvement program. The present study creates a roadmap for easy identification and a better understanding of various transporters, which can be utilized as suitable targets for transporter engineering in future research.

Physiological and molecular responses to combinatorial iron and phosphate deficiencies in hexaploid wheat seedlings

Iron (Fe) and phosphorus (P) are the essential mineral nutrients for plant growth and development. However, the molecular interaction of the Fe and P pathways in crops remained largely obscure. In this study, we provide a comprehensive physiological and molecular analysis of hexaploid wheat response to single (Fe, P) and its combinatorial deficiencies. Our data showed that inhibition of the primary root growth occurs in response to Fe deficiency; however, growth was rescued when combinatorial deficiencies occurred. Analysis of RNAseq revealed that distinct molecular rearrangements during combined deficiencies with predominance for genes related to metabolic pathways and secondary metabolite biosynthesis primarily include genes for UDP-glycosyltransferase, cytochrome-P450s, and glutathione metabolism. Interestingly, the Fe-responsive cis-regulatory elements in the roots in Fe stress conditions were enriched compared to the combined stress. Our metabolome data also revealed the accumulation of distinct metabolites such as amino-isobutyric acid, arabinonic acid, and aconitic acid in the combined stress environment. Overall, these results are essential in developing new strategies to improve the resilience of crops in limited nutrients.

Comparative Transcriptomics of Lowland Rice Varieties Uncovers Novel Candidate Genes for Adaptive Iron Excess Tolerance

Iron (Fe) toxicity is a major challenge for plant cultivation in acidic waterlogged soil environments, where lowland rice is a major staple food crop. Only few studies have addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance. Out of 16 lowland rice varieties, we identified a pair of contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. The two lines differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation and Fe and metal contents. These responses were likely due to genetic origin as they were mirrored by differential gene expression patterns, obtained through RNA sequencing, and corresponding gene ontology term enrichment in tolerant vs. susceptible lines. Thirty-five genes of the metal homeostasis category, mainly root expressed, showed differential transcriptomic profiles suggestive of an induced tolerance mechanism. Twenty-two out of these 35 metal homeostasis genes were present in selection sweep genomic regions, in breeding signatures, and/or differentiated during rice domestication. These findings suggest that Fe excess tolerance is an important trait in the domestication of lowland rice, and the identified genes may further serve to design the targeted Fe tolerance breeding of rice crops.

Modulation of Phosphate Deficiency-Induced Metabolic Changes by Iron Availability in Arabidopsis thaliana

Concurrent suboptimal supply of several nutrients requires the coordination of nutrient-specific transcriptional, phenotypic, and metabolic changes in plants in order to optimize growth and development in most agricultural and natural ecosystems. Phosphate (P_i) and iron (Fe) deficiency induce overlapping but mostly opposing transcriptional and root growth responses in Arabidopsis thaliana. On the metabolite level, P_i deficiency negatively modulates Fe deficiency-induced coumarin accumulation, which is controlled by Fe as well as P_i deficiency response regulators. Here, we report the impact of Fe availability on seedling growth under P_i limiting conditions and on P_i deficiency-induced accumulation of amino acids and organic acids, which play important roles in P_i use efficiency. Fe deficiency in P_i replete conditions hardly changed growth and metabolite profiles in roots and shoots of Arabidopsis thaliana, but partially rescued growth under conditions of P_i starvation and severely modulated P_i deficiency-induced metabolic adjustments. Analysis of T-DNA insertion lines revealed the concerted coordination of metabolic profiles by regulators of Fe (FIT, bHLH104, BRUTUS, PYE) as well as of P_i (SPX1, PHR1, PHL1, bHLH32) starvation responses. The results show the interdependency of P_i and Fe availability and the interplay between P_i and Fe starvation signaling on the generation of plant metabolite profiles.

Metabolic interactions in beneficial microbe recruitment by plants

During millions of years of evolution, land plants and microorganisms have established elaborate partnerships. Microbes play essential roles in plant fitness and help plants cope with environmental challenges. Vice versa, plants provide the microbes with a niche and food. In the soil, a complex network of interactions mediated by metabolic signals drives the relationship between plants and microbes. Here, we review the roles of metabolic signaling in the plant-microbiome interaction. We discuss how plant-produced small molecules are involved in the recruitment of the microbiome. Also the microbial partners in this relationship use small molecules, such as quorum sensing molecules and volatiles for intra-species and inter-species communication. We give an overview of the regulation of the biosynthesis, secretion and perception of both plant and microbial small molecules and discuss the examples of biotechnological approaches to engineer the plant-microbiome interaction by targeting these metabolic dialogues. Ultimately, an improved understanding of the plant-microbiome interaction and engineering possibilities will pave the way to a more sustainable agriculture.

Inhibition of nitric oxide production under alkaline conditions regulates iron homeostasis in rice

Rice is one of the most susceptible plants to iron (Fe) deficiency under neutral and alkaline conditions. Alkaline stress induces H₂ O₂ production and increases the deposition of Fe on the root surface, which causes leaf chlorosis and Fe deficiency in rice. Gene chip and qRT-PCR analysis indicated that the expression of the nitrate reductase (NR) genes were downregulated by alkaline treatment, which resulted in significantly decreased nitrate activity and nitric oxide (NO) production in the epidermis and stele, where H₂ O₂ accumulated. In contrast, treatment with sodium nitroprusside (SNP), a NO donor, strongly alleviated alkaline-induced Fe deficiency by limiting Fe plaque formation. Increasing the NO signal significantly reduced the accumulation of H₂ O₂ and the lignin barrier but enhanced phenolic acid secretion in the root epidermis and stele under alkaline conditions. The secreted phenolic acid effectively mobilized the apoplast Fe and increased Fe uptake in roots, thereby alleviating the Fe-deficiency response and downregulating the expressions of Fe-uptake genes under alkaline conditions. In conclusion, alkaline stress inhibits NR activity and NO production in the roots of rice, which play vital roles in the mobilization of the apoplast Fe by regulation of H₂ O₂ and phenolic acid concentrations.

Ferroportin 3 is a dual-targeted mitochondrial/chloroplast iron exporter necessary for iron homeostasis in Arabidopsis

Mitochondria and chloroplasts are organelles with high iron demand that are particularly susceptible to iron-induced oxidative stress. Despite the necessity of strict iron regulation in these organelles, much remains unknown about mitochondrial and chloroplast iron transport in plants. Here, we propose that Arabidopsis ferroportin 3 (FPN3) is an iron exporter that is dual-targeted to mitochondria and chloroplasts. FPN3 is expressed in shoots, regardless of iron conditions, but its transcripts accumulate under iron deficiency in roots. fpn3 mutants cannot grow as well as the wild type under iron-deficient conditions and their shoot iron levels are lower compared with the wild type. Analyses of iron homeostasis gene expression in fpn3 mutants and inductively coupled plasma mass spectrometry (ICP-MS) measurements show that iron levels in the mitochondria and chloroplasts are increased relative to the wild type, consistent with the proposed role of FPN3 as a mitochondrial/plastid iron exporter. In iron-deficient fpn3 mutants, abnormal mitochondrial ultrastructure was observed, whereas chloroplast ultrastructure was not affected, implying that FPN3 plays a critical role in the mitochondria. Overall, our study suggests that FPN3 is essential for optimal iron homeostasis.

Interplay between Coumarin Accumulation, Iron Deficiency and Plant Resistance to Dickeya spp

Coumarins belong to a group of secondary metabolites well known for their high biological activities including antibacterial and antifungal properties. Recently, an important role of coumarins in plant resistance to pathogens and their release into the rhizosphere upon pathogen infection was discovered. It is also well documented that coumarins play a crucial role in the Arabidopsis thaliana growth under Fe-limited conditions. However, the mechanisms underlying interplay between plant resistance, accumulation of coumarins and Fe status, remain largely unknown. In this work, we investigated the effect of both mentioned factors on the disease severity using the model system of Arabidopsis/Dickeya spp. molecular interactions. We evaluated the disease symptoms in Arabidopsis plants, wild-type Col-0 and its mutants defective in coumarin accumulation, grown in hydroponic cultures with contrasting Fe regimes and in soil mixes. Under all tested conditions, Arabidopsis plants inoculated with Dickeya solani IFB0099 strain developed more severe disease symptoms compared to lines inoculated with Dickeya dadantii 3937. We also showed that the expression of genes encoding plant stress markers were strongly affected by D. solani IFB0099 infection. Interestingly, the response of plants to D. dadantii 3937 infection was genotype-dependent in Fe-deficient hydroponic solution.

Low nitrate alleviates iron deficiency by regulating iron homeostasis in apple

Iron (Fe) is an essential element for plant growth, development and metabolism. Due to its lack of solubility and low bioavailability in soil, Fe levels are usually far below the optimum amount for most plants' growth and development. In apple production, excessive use of nitrogen fertilizer may cause iron chlorosis symptoms in the newly growing leaves, but the regulatory mechanisms underlying this phenomenon are unclear. In this study, low nitrate (NO₃^- , LN) application alleviated the symptoms of Fe deficiency and promoted lower rhizosphere pH, which was beneficial for root Fe acquisition. At the same time, LN treatment increased citrate and abscisic acid accumulation in roots, which promoted Fe transport from root to shoot and maintained Fe homeostasis. Moreover, qRT-PCR analysis showed that nitrate application caused differential expression of genes related to Fe uptake and transport, as well as transcriptional regulators. In summary, our data reveal that low nitrate alleviated Fe deficiency through multiple pathways, demonstrating a new option for minimizing Fe deficiency by regulating the balance between nutrients.

Ethylene and Nitric Oxide Involvement in the Regulation of Fe and P Deficiency Responses in Dicotyledonous Plants

Iron (Fe) and phosphorus (P) are two essential elements for plant growth. Both elements are abundant in soils but with poor availability for plants, which favor their acquisition by developing morphological and physiological responses in their roots. Although the regulation of the genes related to these responses is not totally known, ethylene (ET) and nitric oxide (NO) have been involved in the activation of both Fe-related and P-related genes. The common involvement of ET and NO suggests that they must act in conjunction with other specific signals, more closely related to each deficiency. Among the specific signals involved in the regulation of Fe- or P-related genes have been proposed Fe-peptides (or Fe ion itself) and microRNAs, like miR399 (P), moving through the phloem. These Fe- or P-related phloem signals could interact with ET/NO and confer specificity to the responses to each deficiency, avoiding the induction of the specific responses when ET/NO increase due to other nutrient deficiencies or stresses. Besides the specificity conferred by these signals, ET itself could confer specificity to the responses to Fe- or P-deficiency by acting through different signaling pathways in each case. Given the above considerations, there are preliminary results suggesting that ET could regulate different nutrient responses by acting both in conjunction with other signals and through different signaling pathways. Because of the close relationship among these two elements, a better knowledge of the physiological and molecular basis of their interaction is necessary to improve their nutrition and to avoid the problems associated with their misuse. As examples of this interaction, it is known that Fe chlorosis can be induced, under certain circumstances, by a P over- fertilization. On the other hand, Fe oxides can have a role in the immobilization of P in soils. Qualitative and quantitative assessment of the dynamic of known Fe- and P-related genes expression, selected ad hoc and involved in each of these deficiencies, would allow us to get a profound knowledge of the processes that regulate the responses to both deficiencies. The better knowledge of the regulation by ET of the responses to these deficiencies is necessary to properly understand the interactions between Fe and P. This will allow the obtention of more efficient varieties in the absorption of P and Fe, and the use of more rational management techniques for P and Fe fertilization. This will contribute to minimize the environmental impacts caused by the use of P and Fe fertilizers (Fe chelates) in agriculture and to adjust the costs for farmers, due to the high prices and/or scarcity of Fe and P fertilizers. This review aims to summarize the latest advances in the knowledge about Fe and P deficiency responses, analyzing the similarities and differences among them and considering the interactions among their main regulators, including some hormones (ethylene) and signaling substances (NO and GSNO) as well as other P- and Fe-related signals.

Genome-wide analysis of ATP-binding cassette transporter provides insight to genes related to bioactive metabolite transportation in Salvia miltiorrhiza

BACKGROUND

ATP-binding cassette (ABC) transporters have been found to play important roles in metabolic transport in plant cells, influencing subcellular compartmentalisation and tissue distribution of these metabolic compounds. Salvia miltiorrhiza Bunge, known as Danshen in traditional Chinese medicine, is a highly valued medicinal plant used to treat cardiovascular and cerebrovascular diseases. The dry roots and rhizomes of S. miltiorrhiza contain biologically active secondary metabolites of tanshinone and salvianolic acid. Given an assembled and annotated genome and a set of transcriptome data of S. miltiorrhiza, we analysed and identified the candidate genes that likely involved in the bioactive metabolite transportation of this medicinal plant, starting with the members of the ABC transporter family.

RESULTS

A total of 114 genes encoding ABC transporters were identified in the genome of S. miltiorrhiza. All of these ABC genes were divided into eight subfamilies: 3ABCA, 31ABCB, 14ABCC, 2ABCD, 1ABCE, 7ABCF, 46ABCG, and 10 ABCI. Gene expression analysis revealed tissue-specific expression profiles of these ABC transporters. In particular, we found 18 highly expressed transporters in the roots of S. miltiorrhiza, which might be involved in transporting the bioactive compounds of this medicinal plant. We further investigated the co-expression profiling of these 18 genes with key enzyme genes involved in tanshinone and salvianolic acid biosynthetic pathways using quantitative reverse transcription polymerase chain reaction (RT-qPCR). From this RT-qPCR validation, we found that three ABC genes (SmABCG46, SmABCG40, and SmABCG4) and another gene (SmABCC1) co-expressed with the key biosynthetic enzymes of these two compounds, respectively, and thus might be involved in tanshinone and salvianolic acid transport in root cells. In addition, we predicted the biological functions of S. miltiorrhiza ABC transporters using phylogenetic relationships and analysis of the transcriptome to find biological functions.

CONCLUSIONS

Here, we present the first systematic analysis of ABC transporters in S. miltiorrhiza and predict candidate transporters involved in bioactive compound transportation in this important medicinal plant. Using genome-wide identification, transcriptome profile analysis, and phylogenetic relationships, this research provides a new perspective on the critical functions of ABC transporters in S. miltiorrhiza.

Genome-wide analysis of ATP-binding cassette transporter provides insight to genes related to bioactive metabolite transportation in Salvia miltiorrhiza

BACKGROUND

ATP-binding cassette (ABC) transporters have been found to play important roles in metabolic transport in plant cells, influencing subcellular compartmentalisation and tissue distribution of these metabolic compounds. Salvia miltiorrhiza Bunge, known as Danshen in traditional Chinese medicine, is a highly valued medicinal plant used to treat cardiovascular and cerebrovascular diseases. The dry roots and rhizomes of S. miltiorrhiza contain biologically active secondary metabolites of tanshinone and salvianolic acid. Given an assembled and annotated genome and a set of transcriptome data of S. miltiorrhiza, we analysed and identified the candidate genes that likely involved in the bioactive metabolite transportation of this medicinal plant, starting with the members of the ABC transporter family.

RESULTS

A total of 114 genes encoding ABC transporters were identified in the genome of S. miltiorrhiza. All of these ABC genes were divided into eight subfamilies: 3ABCA, 31ABCB, 14ABCC, 2ABCD, 1ABCE, 7ABCF, 46ABCG, and 10 ABCI. Gene expression analysis revealed tissue-specific expression profiles of these ABC transporters. In particular, we found 18 highly expressed transporters in the roots of S. miltiorrhiza, which might be involved in transporting the bioactive compounds of this medicinal plant. We further investigated the co-expression profiling of these 18 genes with key enzyme genes involved in tanshinone and salvianolic acid biosynthetic pathways using quantitative reverse transcription polymerase chain reaction (RT-qPCR). From this RT-qPCR validation, we found that three ABC genes (SmABCG46, SmABCG40, and SmABCG4) and another gene (SmABCC1) co-expressed with the key biosynthetic enzymes of these two compounds, respectively, and thus might be involved in tanshinone and salvianolic acid transport in root cells. In addition, we predicted the biological functions of S. miltiorrhiza ABC transporters using phylogenetic relationships and analysis of the transcriptome to find biological functions.

CONCLUSIONS

Here, we present the first systematic analysis of ABC transporters in S. miltiorrhiza and predict candidate transporters involved in bioactive compound transportation in this important medicinal plant. Using genome-wide identification, transcriptome profile analysis, and phylogenetic relationships, this research provides a new perspective on the critical functions of ABC transporters in S. miltiorrhiza.

ATP binding cassette proteins ABCG37 and ABCG33 function as potassium-independent cesium uptake carriers in Arabidopsis roots

Radiocesium accumulated in the soil by nuclear accidents is a major environmental concern. The transport process of cesium (Cs⁺) is tightly linked to the indispensable plant nutrient potassium (K⁺) as they both belong to the group I alkali metals with similar chemical properties. Most of the transporters that had been characterized to date as Cs⁺ transporters are directly or indirectly linked to K⁺. Using a combinatorial approach of physiology, genetics, cell biology, and root uptake assay, here we identified two ATP-binding cassette (ABC) proteins, ABCG37 and ABCG33, as facilitators of Cs⁺ influx. A gain-of-function mutant of ABCG37 (abcg37-1) showed increased sensitivity to Cs⁺-induced root growth inhibition, while the double knockout mutant of ABCG33 and ABCG37 (abcg33-1abcg37-2) showed resistance, whereas the single loss-of-function mutants of ABCG33 and ABCG37 did not show any alteration in Cs⁺ response. In planta short-term radioactive Cs⁺-uptake assay along with growth and uptake assays in a heterologous system confirmed ABCG33 and ABCG37 as Cs⁺-uptake carriers. Potassium response and content were unaffected in the double-mutant background and yeast cells lacking potassium-uptake carriers transformed with ABCG33 and ABCG37 failed to grow in the absence of K⁺, confirming that Cs⁺ uptake by ABCG33 and ABCG37 is independent of K⁺. Collectively, this work identified two ABC proteins as new Cs⁺-influx carriers that act redundantly and independent of the K⁺-uptake pathway.

Understanding Plant Social Networking System: Avoiding Deleterious Microbiota but Calling Beneficials

Plant association with microorganisms elicits dramatic effects on the local phytobiome and often causes systemic and transgenerational modulation on plant immunity against insect pests and microbial pathogens. Previously, we introduced the concept of the plant social networking system (pSNS) to highlight the active involvement of plants in the recruitment of potentially beneficial microbiota upon exposure to insects and pathogens. Microbial association stimulates the physiological responses of plants and induces the development of their immune mechanisms while interacting with multiple enemies. Thus, beneficial microbes serve as important mediators of interactions among multiple members of the multitrophic, microscopic and macroscopic communities. In this review, we classify the steps of pSNS such as elicitation, signaling, secreting root exudates, and plant protection; summarize, with evidence, how plants and beneficial microbes communicate with each other; and also discuss how the molecular mechanisms underlying this communication are induced in plants exposed to natural enemies. Collectively, the pSNS modulates robustness of plant physiology and immunity and promotes survival potential by helping plants to overcome the environmental and biological challenges.

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.

Mechanisms underlying iron deficiency-induced resistance against pathogens with different lifestyles

Iron (Fe) is a poorly available mineral nutrient which affects the outcome of many cross-kingdom interactions. In Arabidopsis thaliana, Fe starvation limits infection by necrotrophic pathogens. Here, we report that Fe deficiency also reduces disease caused by the hemi-biotrophic bacterium Pseudomonas syringae and the biotrophic oomycete Hyaloperonospora arabidopsidis, indicating that Fe deficiency-induced resistance is effective against pathogens with different lifestyles. Furthermore, we show that Fe deficiency-induced resistance is not caused by withholding Fe from the pathogen but is a plant-mediated defense response that requires activity of ethylene and salicylic acid. Because rhizobacteria-induced systemic resistance (ISR) is associated with a transient up-regulation of the Fe deficiency response, we tested whether Fe deficiency-induced resistance and ISR are similarly regulated. However, Fe deficiency-induced resistance functions independently of the ISR regulators MYB72 and BGLU42, indicating that both types of induced resistance are regulated in a different manner. Mutants opt3 and frd1, which display misregulated Fe homeostasis under Fe-sufficient conditions, show disease resistance levels comparable with those of Fe-starved wild-type plants. Our results suggest that disturbance of Fe homeostasis, through Fe starvation stress or other non-homeostatic conditions, is sufficient to prime the plant immune system for enhanced defense.

Transcriptional integration of plant responses to iron availability

Iron is one of the most important micronutrients for plant growth and development. It functions as the enzyme cofactor or component of electron transport chains in various vital metabolic processes, including photosynthesis, respiration, and amino acid biosynthesis. To maintain iron homeostasis, and therefore prevent any deficiency or excess that could be detrimental, plants have evolved complex transcriptional regulatory networks to tightly control iron uptake, translocation, assimilation, and storage. These regulatory networks are composed of various transcription factors; among them, members of the basic helix-loop-helix (bHLH) family play an essential role. Here, we first review recent advances in understanding the roles of bHLH transcription factors involved in the regulatory cascade controlling iron homeostasis in the model plant Arabidopsis, and extend this understanding to rice and other plant species. The importance of other classes of transcription factors will also be discussed. Second, we elaborate on the post-translational mechanisms involved in the regulation of these regulatory networks. Finally, we provide some perspectives on future research that should be conducted in order to precisely understand how plants control the homeostasis of this micronutrient.

Transcriptome Signatures in Pseudomonas simiae WCS417 Shed Light on Role of Root-Secreted Coumarins in Arabidopsis-Mutualist Communication

Pseudomonas simiae WCS417 is a root-colonizing bacterium with well-established plant-beneficial effects. Upon colonization of Arabidopsis roots, WCS417 evades local root immune responses while triggering an induced systemic resistance (ISR) in the leaves. The early onset of ISR in roots shows similarities with the iron deficiency response, as both responses are associated with the production and secretion of coumarins. Coumarins can mobilize iron from the soil environment and have a selective antimicrobial activity that impacts microbiome assembly in the rhizosphere. Being highly coumarin-tolerant, WCS417 induces the secretion of these phenolic compounds, likely to improve its own niche establishment, while providing growth and immunity benefits for the host in return. To investigate the possible signaling function of coumarins in the mutualistic Arabidopsis-WCS417 interaction, we analyzed the transcriptome of WCS417 growing in root exudates of coumarin-producing Arabidopsis Col-0 and the coumarin-biosynthesis mutant f6′h1. We found that coumarins in F6′H1-dependent root exudates significantly affected the expression of 439 bacterial genes (8% of the bacterial genome). Of those, genes with functions related to transport and metabolism of carbohydrates, amino acids, and nucleotides were induced, whereas genes with functions related to cell motility, the bacterial mobilome, and energy production and conversion were repressed. Strikingly, most genes related to flagellar biosynthesis were down-regulated by F6′H1-dependent root exudates and we found that application of selected coumarins reduces bacterial motility. These findings suggest that coumarins’ function in the rhizosphere as semiochemicals in the communication between the roots and WCS417. Collectively, our results provide important novel leads for future functional analysis of molecular processes in the establishment of plant-mutualist interactions.

The Coumarins: Secondary Metabolites Playing a Primary Role in Plant Nutrition and Health

Although abundant in soils, iron (Fe) is poorly bioavailable for plants. Improving Fe uptake in crops, enabling them to grow in Fe-depleted soils, has become a major focal interest. The secretion of Fe-mobilizing coumarins by plant roots recently emerged as an important factor allowing nongrass species to cope with low Fe bioavailability. The main molecular actors involved in the biosynthesis and secretion of coumarins have been identified, but the precise regulatory mechanisms that tune their production remain poorly understood. Here, we review the recent progress in coumarin synthesis and transport in plants and future research directions to gain knowledge of these mechanisms, which will offer novel opportunities for improving plant growth and health and for generating Fe-fortified crops.

PAP/SAL1 retrograde signaling pathway modulates iron deficiency response in alkaline soils

Iron (Fe) is an essential micronutrient for plants and is present abundantly in the Earth's crust. However, Fe bioavailability in alkaline soils is low due to the decreased solubility of the ferric ions. Previously, we have demonstrated the relationship between the PAP/SAL1 retrograde signaling pathway, the activity of Strategy I Fe uptake genes (FIT, FRO2, IRT1), and ethylene signaling. In this work, we have characterized mutant lines that are deficient in this retrograde signaling pathway and their ability to grow in alkaline soils. This adverse growth condition caused less impact on mutant plants, which showed less reduced rosette area, and higher carotenoid, chlorophyll and Fe content than wild-type plants. Several genes involved in the biosynthesis and excretion of secondary metabolites derived from the phenylpropanoid pathway, which improve Fe uptake, were elevated in mutant plants. Finally, we observed an increase in excreted fluorescent phenolic compounds in mutant lines compared to wild-type plants. In this way, PAP/SAL1 mutants showed alterations in the biosynthesis of metabolites that mobilize Fe, which ultimately improved these plants ability to grow in alkaline soils. Results agree with the existence of a link between the PAP/SAL1 retrograde signaling pathway and the regulation of Fe deficiency responses in Arabidopsis.

The functional analysis of ABCG transporters in the adaptation of pigeon pea (Cajanus cajan) to abiotic stresses

ATP-binding cassette (ABC) transporters are a class of proteins found in living organisms that mediate transmembrane transport by hydrolyzing ATP. They play a vital role in the physiological processes of growth and development in plants. The most numerous sub-type transporter in the ABC transporter family is the ABCG group and which have the most complex function in a plant’s response to abiotic stresses. Our study focused on the effect of ABCG transporters in the adaptation of the pigeon pea to adverse environments (such as drought, salt, temperature, etc.). We conducted a functional analysis of ABCG transporters in the pigeon pea and their role in response to abiotic stresses. A total of 51 ABCG genes (CcABCGs) were identified, and phylogenetic analysis was conducted. We also identified the physicochemical properties of the encoded proteins, predicted their subcellular localization, and identified of the conserved domains. Expression analysis showed that ABCG genes have different expression profiles with tissues and abiotic stresses. Our results showed that CcABCG28 was up-regulated at low temperatures, and CcABCG7 was up-regulated with drought and aluminum stress. The initial results revealed that ABCG transporters are more effective in the abiotic stress resistance of pigeon peas, which improves our understanding of their application in abiotic stress resistance.

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

Iron (Fe) is a major micronutrient and is required for plant growth and development. Nongrass species have evolved a reduction-based strategy to solubilize and take up Fe. The secretion of Fe-mobilizing coumarins (e.g. fraxetin, esculetin and sideretin) by plant roots plays an important role in this process. Although the biochemical mechanisms leading to their biosynthesis have been well described, very little is known about their cellular and subcellular localization or their mobility within plant tissues. Spectral imaging was used to monitor, in Arabidopsis thaliana, the in planta localization of Fe-mobilizing coumarins and scopolin. Molecular, genetic and biochemical approaches were also used to investigate the dynamics of coumarin accumulation in roots. These approaches showed that root hairs play a major role in scopoletin secretion, whereas fraxetin and esculetin secretion occurs through all epidermis cells. The findings of this study also showed that the transport of coumarins from the cortex to the rhizosphere relies on the PDR9 transporter under Fe-deficient conditions. Additional experiments support the idea that coumarins move throughout the plant body via the xylem sap and that several plant species can take up coumarins present in the surrounding media. Altogether, the data presented here demonstrate that coumarin storage and accumulation in roots is a highly complex and dynamic process.

Iron deficient Medicago scutellata grown in nutrient solution at high pH accumulates and secretes large amounts of flavins

Flavin synthesis and secretion is an integral part of the toolbox of root-borne Fe facilitators used by Strategy I species upon Fe deficiency. The Fe-deficiency responses of the wild legume Medicago scutellata grown in nutrient solution have been studied at two different pH values (5.5 and 7.5). Parameters studied include leaf chlorophyll, nutrient solution pH, concentrations and contents of micronutrients, flavin accumulation in roots, flavin export to the medium, and root ferric chelate reductase and acidification activities. Results show that M. scutellata behaves upon Fe deficiency as a Strategy I species, with a marked capacity for synthesizing flavins (riboflavin and three hydroxylated riboflavin derivatives), which becomes more intense at high pH. Results also show that this species is capable of exporting a large amount of flavins to the external medium, both at pH 5.5 and 7.5. This is the first report of a species having a major flavin secretion at pH 7.5, in contrast with the very low flavin secretion found in other flavin-producing species such as Beta vulgaris and M. truncatula. These results provide further support to the hypothesis that flavin secretion is relevant for Fe acquisition at high pH, and open the possibility to improve the Fe-efficiency responses in legumes of agronomic interest.

Coumarin Communication Along the Microbiome-Root-Shoot Axis

Plants shape their rhizosphere microbiome by secreting root exudates into the soil environment. Recently, root-exuded coumarins were identified as novel players in plant-microbiome communication. Beneficial members of the root-associated microbiome stimulate coumarin biosynthesis in roots and their excretion into the rhizosphere. The iron-mobilizing activity of coumarins facilitates iron uptake from the soil environment, while their selective antimicrobial activity shapes the root microbiome, resulting in promotion of plant growth and health. Evidence is accumulating that, in analogy to strigolactones and flavonoids, coumarins may act in microbiome-to-root-to-shoot signaling events. Here, we review this multifaceted role of coumarins in bidirectional chemical communication along the microbiome-root-shoot axis.

The ABC transporter G subfamily in Arabidopsis thaliana

ABC transporters are ubiquitously present in all kingdoms and mediate the transport of a large spectrum of structurally different compounds. Plants possess high numbers of ABC transporters in relation to other eukaryotes; the ABCG subfamily in particular is extensive. Earlier studies demonstrated that ABCG transporters are involved in important processes influencing plant fitness. This review summarizes the functions of ABCG transporters present in the model plant Arabidopsis thaliana. These transporters take part in diverse processes such as pathogen response, diffusion barrier formation, or phytohormone transport. Studies involving knockout mutations reported pleiotropic phenotypes of the mutants. In some cases, different physiological roles were assigned to the same protein. The actual transported substrate(s), however, still remain to be determined for the majority of ABCG transporters. Additionally, the proposed substrate spectrum of different ABCG proteins is not always reflected by sequence identities between ABCG members. Applying only reverse genetics is thereby insufficient to clearly identify the substrate(s). We therefore stress the importance of in vitro studies in addition to in vivo studies in order to (i) clarify the substrate identity; (ii) determine the transport characteristics including directionality; and (iii) identify dimerization partners of the half-size proteins, which might in turn affect substrate specificity.

Importance of the Rhizosphere Microbiota in Iron Biofortification of Plants

Increasing the iron content of plant products and iron assimilability represents a major issue for human nutrition and health. This is also a major challenge because iron is not readily available for plants in most cultivated soils despite its abundance in the Earth's crust. Iron biofortification is defined as the enhancement of the iron content in edible parts of plants. This biofortification aims to reach the objectives defined by world organizations for human nutrition and health while being environment friendly. A series of options has been proposed to enhance plant iron uptake and fight against hidden hunger, but they all show limitations. The present review addresses the potential of soil microorganisms to promote plant iron nutrition. Increasing knowledge on the plant microbiota and plant-microbe interactions related to the iron dynamics has highlighted a considerable contribution of microorganisms to plant iron uptake and homeostasis. The present overview of the state of the art sheds light on plant iron uptake and homeostasis, and on the contribution of plant-microorganism (plant-microbe and plant-plant-microbe) interactions to plant nutritition. It highlights the effects of microorganisms on the plant iron status and on the co-occurring mechanisms, and shows how this knowledge may be valued through genetic and agronomic approaches. We propose a change of paradigm based on a more holistic approach gathering plant and microbial traits mediating iron uptake. Then, we present the possible applications in plant breeding, based on plant traits mediating plant-microbe interactions involved in plant iron uptake and physiology.

Membrane transporters: the key drivers of transport of secondary metabolites in plants

This review summarizes the recent updates in the area of transporters of plant secondary metabolites, including their applied aspects in metabolic engineering of economically important secondary metabolites. Plants have evolved biosynthetic pathways to produce structurally diverse secondary metabolites, which serve distinct functions, including defense against pathogens and herbivory, thereby playing a pivotal role in plant ecological interactions. These compounds often display interesting bioactivities and, therefore, have been used as repositories of natural drugs and phytoceuticals for humans. At an elevated level, plant secondary metabolites could be cytotoxic to the plant cell itself; therefore, plants have developed sophisticated mechanisms to sequester these compounds to prevent cytotoxicity. Many of these valuable natural compounds and their precursors are biosynthesized and accumulated at diverse subcellular locations, and few are even transported to sink organs via long-distance transport, implying the involvement of compartmentalization via intra- and intercellular transport mechanisms. The transporter proteins belonging to different families of transporters, especially ATP binding cassette (ABC) and multidrug and toxic compound extrusion (MATE) have been implicated in membrane-mediated transport of certain plant secondary metabolites. Despite increasing reports on the characterization of transporter proteins and their genes, our knowledge about the transporters of several medicinally and economically important plant secondary metabolites is still enigmatic. A comprehensive understanding of the molecular mechanisms underlying the whole route of secondary metabolite transportome, in addition to the biosynthetic pathways, will aid in systematic and targeted metabolic engineering of high-value secondary metabolites. The present review embodies a comprehensive update on the progress made in the elucidation of transporters of secondary metabolites in view of basic and applied aspects of their transport mechanism.

Protein bodies of the endoplasmic reticulum in Arabidopsis thaliana (Brassicaceae): origin, structural and biochemical features, functional significance

History of the discovery, formation, structural and biochemical traits of the protein bodies, derivatives of the granular endoplasmic reticulum (GER) that are known as ER-bodies, are reviewed. The functions of ER-bodies in cell vital activity mainly in Arabidopsis thaliana are reported. The highly specific component of ER-bodies, β-glucosidase enzyme, is described and its protecting role for plants under effect of abiotic and biotic factors is characterized. Based on the analytical review of the literature, it is shown that ER-bodies and the transcription factor NAI2 are unique to species of the family Brassicaceae. The specificity of the system GER – ER-bodies for Brassicaceae and thus the fundamental and applied importance of future research of mechanisms of its functioning in A. thaliana and other Brassicaceae species are emphasized.

Changes in physiological activities and root exudation profile of two grapevine rootstocks reveal common and specific strategies for Fe acquisition

In several cultivation areas, grapevine can suffer from Fe chlorosis due to the calcareous and alkaline nature of soils. This plant species has been described to cope with Fe deficiency by activating Strategy I mechanisms, hence increasing root H⁺ extrusion and ferric-chelate reductase activity. The degree of tolerance exhibited by the rootstocks has been reported to depend on both reactions, but to date, little emphasis has been given to the role played by root exudate extrusion. We studied the behaviour of two hydroponically-grown, tolerant grapevine rootstocks (Ramsey and 140R) in response to Fe deficiency. Under these experimental conditions, the two varieties displayed differences in their ability to modulate morpho-physiological parameters, root acidification and ferric chelate reductase activity. The metabolic profiling of root exudates revealed common strategies for Fe acquisition, including ones targeted at reducing microbial competition for this micronutrient by limiting the exudation of amino acids and sugars and increasing instead that of Fe(III)-reducing compounds. Other modifications in exudate composition hint that the two rootstocks cope with Fe shortage via specific adjustments of their exudation patterns. Furthermore, the presence of 3-hydroxymugenic acid in these compounds suggests that the responses of grapevine to Fe availability are rather diverse and much more complex than those usually described for Strategy I plants.

Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis

Plants benefit from associations with a diverse community of root-colonizing microbes. Deciphering the mechanisms underpinning these beneficial services are of interest for improving plant productivity. We report a plant-beneficial interaction between Arabidopsis thaliana and the root microbiota under iron deprivation that is dependent on the secretion of plant-derived coumarins. Disrupting this pathway alters the microbiota and impairs plant growth in iron-limiting soil. Furthermore, the microbiota improves iron-limiting plant performance via a mechanism dependent on plant iron import and secretion of the coumarin fraxetin. This beneficial trait is strain specific yet functionally redundant across phylogenetic lineages of the microbiota. Transcriptomic and elemental analyses revealed that this interaction between commensals and coumarins promotes growth by relieving iron starvation. These results show that coumarins improve plant performance by eliciting microbe-assisted iron nutrition. We propose that the bacterial root microbiota, stimulated by secreted coumarins, is an integral mediator of plant adaptation to iron-limiting soils.

The role of plant growth-promoting rhizobacteria (PGPR) in improving iron acquisition by altering physiological and molecular responses in quince seedlings

Due to insoluble iron (Fe) sources in soil, limited Fe availability leads to the disruption of the photosynthetic apparatus; this affects the growth and productivity of plants such as quince (Cydonia oblonga) that are very sensitive to low Fe content. Plant growth-promoting rhizobacteria (PGPR) play an important role in the regulation of Fe uptake under its limited availability. Therefore, in this research, two PGPR (Pseudomonas fluorescens and Microccucuce yunnanensis), at two Fe levels [50 μM (Fe-sufficiency) or 5 μM (Fe-deficiency)], were used to investigate the impact of the given bacteria on improving the acquisition of Fe in quince seedlings. Upon Fe-deficiency, the highest shoot and root biomass (7.14 and 6.04 g plant^-1 respectively), the greatest chlorophyll concentration (0.89 mg g^-1FW), and the largest Fe concentrations in roots and shoots (30% and 48.7%, respectively) were shown in the quince treated with M. yunnanensis. Both PGPR increased the root citric acid and the phenolic compound concentration. Two days after Fe-deficiency and PGPR treatments, a 1.5- fold increase, was observed in the expression of HA7. The highest PAL1 gene expression and the greatest PAL activity (95.76 μmol cinnamic acid g^-1FW) were obtained from the M. yunnanensis treatment. The expression of the FRO2 gene was also affected by Fe-deficiency and PGPR treatments, resulting in an increase in the FCR activity and a surge in the Fe concentrations of leaves and roots. It could, therefore, be concluded that the PGPR modulated Fe acquisition in the quince seedlings upon Fe-deficiency by influencing the physico-chemical and molecular responses.

Systematic Investigation of the Effects of Macro-elements and Iron on Soybean Plant Response to Fusarium oxysporum Infection

Nutrient manipulation is a promising strategy for controlling plant diseases in sustainable agriculture. Although many studies have investigated the relationships between certain elements and plant diseases, few have comprehensively explored how differing mineral nutrition levels might affect plant-fungal pathogen interactions, namely plant susceptibility and resistance. Here, we systematically explored the effects of the seven mineral elements that plants require in the greatest amounts for normal development on the susceptibility of soybean plants (Glycine max) to Fusarium oxysporum infection in controlled greenhouse conditions. Nitrogen (N) negligibly affected plant susceptibility to infection in the range 4 to 24 mM for both tested soybean cultivars. At relatively high concentrations, phosphorus (P) increased plant susceptibility to infection, which led to severely reduced shoot and root dry weights. Potassium (K), calcium (Ca), magnesium (Mg), sulfur (S), and iron (Fe) induced plant resistance to infection as their concentrations were increased. For K and Ca, moderate concentrations had a positive effect on plant resistance to the pathogen, whereas relatively high doses of either element adversely affected plant growth and promoted disease symptoms. Further experiments were conducted, assessing disease suppression by selected combinations of macro-elements and Fe at screened concentrations, i.e., K (9 mM) plus Fe (0.2 mM), and S (4 mM) plus Fe (0.2 mM). The disease index was significantly reduced by the combination of K plus Fe. In conclusion, this systematic investigation of soybean plant responses to F. oxysporum infection provides a solid basis for future environmentally-friendly choices for application in soybean disease control programs.

PRC2-mediated H3K27me3 modulates shoot iron homeostasis in Arabidopsis thaliana

Plants use intricate mechanisms to adapt to changing iron conditions because iron is essential and also one of the most limiting nutrients for plant growth. Furthermore, iron is potentially toxic in excess and must be tightly regulated. Previously, we showed that chromatin remodeling via histone 3 lysine 27 trimethylation (H3K27me3) modulates the expression of FIT-dependent genes under iron deficiency in roots. This study builds on our previous findings, showing that H3K27me3 also modulates iron regulation in shoots. In the clf mutant, which lacks the predominant H3K27 tri-methyltransferase, we detected increased iron translocation to shoots under iron deficiency as compared to wild type. Transcriptomic analysis of shoots also revealed differential expression of genes consistent with higher iron levels in clf shoots than wild type shoots under iron-deficient conditions. In addition, we verify that YSL1 and IMA1, two genes involved in signaling iron status from shoots to roots, are direct targets of H3K27me3 and reveal iron-dependent deposition of H3K27me3 on these loci. This study contributes to a better understanding of the molecular mechanisms behind iron regulation in plants, as the effect of PRC2-mediated H3K27me3 on iron homeostasis genes expressed in the shoots has not been previously reported to our knowledge.

Phosphate regulates malate/citrate-mediated iron uptake and transport in apple

The accumulation of iron (Fe) in the apical meristem is considered as a critical factor involved in limiting the elongation of roots under low phosphate (Pi) conditions. Furthermore, the antagonism between Fe and Pi largely affects the effective utilization of Fe. Although the lack of Pi serves to increase the effectiveness of Fe in rice under both Fe-sufficient and Fe-deficient conditions, the underlying physiological mechanism governing this phenomenon is still unclear. In this study, we found that low Pi alleviated the Fe-deficiency phenotype in apples. Additionally, low Pi treatments increased ferric-chelated reductase (FCR) activity in the rhizosphere, promoted proton exocytosis, and enhanced the Fe concentration in both the roots and shoots. In contrast, high Pi treatments inhibited this process. Under conditions of low Pi, malate and citrate exudation from apple roots occurred under both Fe-sufficient and Fe-deficient conditions. In addition, treatment with 0.5 mM malate and citrate effectively alleviated the Fe and Pi deficiencies. Taken together, these data support the conclusion that a low Pi supply promotes organic acids exudation and enhances Fe absorption during Fe deficiency in apples.

Specialized phenolic compounds in seeds: structures, functions, and regulations

Plants produce a huge diversity of specialized metabolites (SM) throughout their life cycle that play important physiological and ecological functions. SM can protect plants and seeds against diseases, predators, and abiotic stresses, or support their interactions with beneficial or symbiotic organisms. They also have strong impacts on human nutrition and health. Despite this importance, the biosynthesis and biological functions of most of the SM remain elusive and their diversity and/or quantity have been reduced in most crops during domestication. Seeds present a large number of SM that are important for their physiological, agronomic, nutritional or industrial qualities and hence, provide interesting models for both studying biosynthesis and producing large amounts of specialized metabolites. For instance, phenolics are abundant and widely distributed in seeds. More specifically, flavonoid pathway has been instrumental for understanding environmental or developmental regulations of specialized metabolic pathways, at the molecular and cellular levels. Here, we summarize current knowledge on seed phenolics as model, and discuss how recent progresses in omics approaches could help to further characterize their diversity, regulations, and the underlying molecular mechanisms involved.

Single and Combined Fe and S Deficiency Differentially Modulate Root Exudate Composition in Tomato: A Double Strategy for Fe Acquisition?

Fe chlorosis is considered as one of the major constraints on crop growth and yield worldwide, being particularly worse when associated with S shortage, due to the tight link between Fe and S. Plant adaptation to inadequate nutrient availabilities often relies on the release of root exudates that enhance nutrients, mobilization from soil colloids and favour their uptake by roots. This work aims at characterizing the exudomic profile of hydroponically grown tomato plants subjected to either single or combined Fe and S deficiency, as well as at shedding light on the regulation mechanisms underlying Fe and S acquisition processes by plants. Root exudates have been analysed by untargeted metabolomics, through liquid chromatography-mass spectrometry as well as gas chromatography-mass spectrometry following derivatization. More than 200 metabolites could be putatively annotated. Venn diagrams show that 23%, 10% and 21% of differential metabolites are distinctively modulated by single Fe deficiency, single S deficiency or combined Fe-S deficiency, respectively. Interestingly, for the first time, a mugineic acid derivative is detected in dicot plants root exudates. The results seem to support the hypothesis of the co-existence of the two Fe acquisition strategies in tomato plants.