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

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

Recent advances in unraveling the mystery of combined nutrient stress in plants.

Efficiently regulating growth to adapt to varying resource availability is crucial for organisms, including plants. In particular, the acquisition of essential nutrients is vital for plant development, as a shortage of just one nutrient can significantly decrease crop yield. However, plants constantly experience fluctuations in the presence of multiple essential mineral nutrients, leading to combined nutrient stress conditions. Unfortunately, our understanding of how plants perceive and respond to these multiple stresses remains limited. Unlocking this mystery could provide valuable insights and help enhance plant nutrition strategies. This review focuses specifically on the regulation of phosphorous homeostasis in plants, with a primary emphasis on recent studies that have shed light on the intricate interactions between phosphorous and other essential elements, such as nitrogen, iron, and zinc, as well as non-essential elements like aluminum and sodium. By summarizing and consolidating these findings, this review aims to contribute to a better understanding of how plants respond to and cope with combined nutrient stress.

The transcription factor OsbZIP48 governs rice responses to zinc deficiency.

Zinc (Zn) deficiency is the most prevalent micronutrient disorder in rice and leads to delayed development and decreased yield. Nevertheless, despite its primary importance, how rice responds to Zn deficiency remains poorly understood. This study presents genetic evidence supporting the crucial role of OsbZIP48 in regulating rice's response to Zn deficiency, consistent with earlier findings in the model plant Arabidopsis. Genetic inactivation of OsbZIP48 in rice seedlings resulted in heightened sensitivity to Zn deficiency and reduced Zn translocation from roots to shoots. Consistently, OsbZIP48 was constitutively expressed in roots, slightly induced by Zn deficiency in shoots and localized into nuclei induced by Zn deficiency. Comparative transcriptome analysis of the wild-type plants and osbzip48 mutant grown under Zn deficiency enabled the identification of OsbZIP48 target genes, including key Zn transporter genes (OsZIP4 and OsZIP8). We demonstrated that OsbZIP48 controlled the expressions of these genes by directly binding to their promoters, specifically to the Zn deficiency response element motif. This study establishes OsbZIP48 as a critical transcription factor in rice's response to Zn deficiency, offering valuable insights for developing Zn-biofortified rice varieties to combat global Zn limitation.

The transcription factor OsSPL9 endows rice with copper deficiency resilience.

Copper (Cu) is a crucial micronutrient essential for the growth and development of plants. Rice exhibits remarkable resistance to Cu deficiency, but the underlying molecular mechanisms are not well understood. In this study, we reveal that the plant's ability to withstand Cu deficiency is orchestrated by a transcription factor known as OsSPL9. We have demonstrated that OsSPL9 functions as a central regulator of Cu homeostasis. Disrupting OsSPL9 through knockout significantly reduced the plant's tolerance to Cu deficiency. As a result, the spl9 mutants exhibited reduced Cu accumulation in their shoots when compared with wild-type plants. This reduction was linked to a disruption in the transport of Cu from older leaves to younger ones. Furthermore, we show that OsSPL9 directly bound to GTAC motifs in the promoters of key genes involved in Cu uptake and transport, as well as Cu-miRNAs, and enhanced their transcription under Cu-deficient conditions. Overall, our findings shed light on the molecular basis of rice resilience to Cu deficiency stress and place the transcription factor OsSPL9 as a master regulator of this response.

Genome-wide association studies and transcriptomics reveal mechanisms explaining the diversity of wheat root responses to nutrient availability.

Nutrient availability profoundly influences plant root system architecture, which critically determines crop productivity. While Arabidopsis has provided important insights into the genetic responses to nutrient deficiency, translating this knowledge to crops, particularly wheat, remains a subject of inquiry. Here, examining a diverse wheat population under varying nitrogen (N), phosphorus (P), potassium (K), and iron (Fe) levels, we uncover a spectrum of root responses, spanning from growth inhibition to stimulation, highlighting genotype-specific strategies. Furthermore, we reveal a nuanced interplay between macronutrient deficiency (N, P, and K) and Fe availability, emphasizing the central role of Fe in modulating root architecture. Through genome-wide association mapping, we identify 11 quantitative trait loci underlying root traits under varying nutrient availabilities, including homologous genes previously validated in Arabidopsis, supporting our findings. In addition, utilizing transcriptomics, ROS imaging, and antioxidant treatment, we uncover that wheat root growth inhibition by nutrient deficiency is attributed to ROS accumulation, akin to the role of ROS in governing Arabidopsis root responses to nutrient deficiency. Therefore, our study reveals the conservation of molecular and physiological mechanisms between Arabidopsis and wheat to adjust root growth to nutrient availability, paving the way for targeted crop improvement strategies aimed at increasing nutrient use efficiency.

A tale of two players: the role of phosphate in iron and zinc homeostatic interactions.

MAIN CONCLUSION: This minireview details the impact of iron-phosphate and zinc-phosphate interactions in plants and provides perspectives for further areas of research regarding nutrient homeostasis. Iron (Fe) and zinc (Zn) are among the most important micronutrients for plant growth and have numerous implications for human health and agriculture. While plants have developed efficient uptake and transport mechanisms for Fe and Zn, emerging research has shown that the availability of other nutrients in the environment influences the homeostasis of Fe and Zn within plants. In this minireview, we present the current knowledge regarding homeostatic interactions of Fe and Zn with the macronutrient phosphorous (P) and the resulting physiological responses to combined deficiencies of these nutrients. Fe and P interactions have been shown to influence root development, photosynthesis, and biological processes aiding Fe uptake. Zn and P interactions also influence root growth, and coordination of Zn-dependent transcriptional regulation contributes to phosphate (Pi) transport in the plant. Understanding homeostatic interactions among these different nutrients is of critical importance to obtain a more complete understanding of plant nutrition in complex soil environments.

OsbHLH061 links TOPLESS/TOPLESS-RELATED repressor proteins with POSITIVE REGULATOR OF IRON HOMEOSTASIS 1 to maintain iron homeostasis in rice.

As excess iron (Fe) is toxic, uptake of this essential micronutrient must be tightly controlled. Previous studies have shown that Oryza sativa (rice) POSITIVE REGULATOR OF IRON HOMEOSTASIS1 (OsPRI1) acts upstream of the iron-related transcription factor 2 (OsIRO2) and OsIRO3 to positively regulate root-to-shoot Fe translocation. However, as expression of OsPRI1 is constitutive it is unclear how the Fe-deficiency response is turned off to prevent toxicity when Fe is sufficient. The bHLH transcription factor OsbHLH061 interacts with OsPRI1, and this study used molecular, genetics, biochemical and physiological approaches to functionally characterise OsbHLH061 and how it affects Fe homeostasis. OsbHLH061 knockout or overexpression lines increase or decrease Fe accumulation in shoots respectively. Mechanistically, OsbHLH061 expression is upregulated by high Fe, and physically interacts with OsPRI1, the OsbHLH061-OsPRI1 complex recruits TOPLESS/TOPLESS-RELATED (OsTPL/TPR) co-repressors to repress OsIRO2 and OsIRO3 expression. The OsbHLH061 ethylene-responsive element-binding factor-associated amphiphilic repression (EAR) motif is required for this transcriptional repression activity. These results define a functional OsTPL/TPR-OsbHLH061-OsPRI1-OsIRO2/3 module that negatively controls long-distance transport of Fe in plants for adaptation to changing Fe environments and maintain Fe homeostasis in rice.

Identification of Molecular Integrators Shows that Nitrogen Actively Controls the Phosphate Starvation Response in Plants.

Nitrogen (N) and phosphorus (P) are key macronutrients sustaining plant growth and crop yield and ensuring food security worldwide. Understanding how plants perceive and interpret the combinatorial nature of these signals thus has important agricultural implications within the context of (1) increased food demand, (2) limited P supply, and (3) environmental pollution due to N fertilizer usage. Here, we report the discovery of an active control of P starvation response (PSR) by a combination of local and long-distance N signaling pathways in plants. We show that, in Arabidopsis (Arabidopsis thaliana), the nitrate transceptor CHLORINA1/NITRATE TRANSPORTER1.1 (CHL1/NRT1.1) is a component of this signaling crosstalk. We also demonstrate that this crosstalk is dependent on the control of the accumulation and turnover by N of the transcription factor PHOSPHATE STARVATION RESPONSE1 (PHR1), a master regulator of P sensing and signaling. We further show an important role of PHOSPHATE2 (PHO2) as an integrator of the N availability into the PSR since the effect of N on PSR is strongly affected in pho2 mutants. We finally show that PHO2 and NRT1.1 influence each other's transcript levels. These observations are summarized in a model representing a framework with several entry points where N signal influence PSR. Finally, we demonstrate that this phenomenon is conserved in rice (Oryza sativa) and wheat (Triticum aestivum), opening biotechnological perspectives in crop plants.

Systems genomics approaches provide new insights into Arabidopsis thaliana root growth regulation under combinatorial mineral nutrient limitation.

The molecular mechanisms by which plants modulate their root growth rate (RGR) in response to nutrient deficiency are largely unknown. Using Arabidopsis thaliana accessions, we analyzed RGR variation under combinatorial mineral nutrient deficiencies involving phosphorus (P), iron (Fe), and zinc (Zn). While -P stimulated early RGR of most accessions, -Fe or -Zn reduced it. The combination of either -P-Fe or -P-Zn led to suppression of the growth inhibition exerted by -Fe or -Zn alone. Surprisingly, root growth responses of the reference accession Columbia (Col-0) were not representative of the species under -P nor -Zn. Using a systems approach that combines GWAS, network-based candidate identification, and reverse genetic screen, we identified new genes that regulate root growth in -P-Fe: VIM1, FH6, and VDAC3. Our findings provide a framework to systematically identifying favorable allelic variations to improve root growth, and to better understand how plants sense and respond to multiple environmental cues.

Wheat inositol pyrophosphate kinase TaVIH2-3B modulates cell-wall composition and drought tolerance in Arabidopsis.

BACKGROUND: Inositol pyrophosphates (PP-InsPs) are high-energy derivatives of inositol, involved in different signalling and regulatory responses of eukaryotic cells. Distinct PP-InsPs species are characterized by the presence of phosphate at a variable number of the 6-carbon inositol ring backbone, and two distinct classes of inositol phosphate kinases responsible for their synthesis have been identified in Arabidopsis, namely ITPKinase (inositol 1,3,4 trisphosphate 5/6 kinase) and PP-IP5Kinase (diphosphoinositol pentakisphosphate kinases). Plant PP-IP5Ks are capable of synthesizing InsP8 and were previously shown to control defense against pathogens and phosphate response signals. However, other potential roles of plant PP-IP5Ks, especially towards abiotic stress, remain poorly understood. RESULTS: Here, we characterized the physiological functions of two Triticum aestivum L. (hexaploid wheat) PPIP5K homologs, TaVIH1 and TaVIH2. We demonstrate that wheat VIH proteins can utilize InsP7 as the substrate to produce InsP8, a process that requires the functional VIH-kinase domains. At the transcriptional level, both TaVIH1 and TaVIH2 are expressed in different wheat tissues, including developing grains, but show selective response to abiotic stresses during drought-mimic experiments. Ectopic overexpression of TaVIH2-3B in Arabidopsis confers tolerance to drought stress and rescues the sensitivity of Atvih2 mutants. RNAseq analysis of TaVIH2-3B-expressing transgenic lines of Arabidopsis shows genome-wide reprogramming with remarkable effects on genes involved in cell-wall biosynthesis, which is supported by the observation of enhanced accumulation of polysaccharides (arabinogalactan, cellulose, and arabinoxylan) in the transgenic plants. CONCLUSIONS: Overall, this work identifies a novel function of VIH proteins, implicating them in modulation of the expression of cell-wall homeostasis genes, and tolerance to water-deficit stress. This work suggests that plant VIH enzymes may be linked to drought tolerance and opens up the possibility of future research into using plant VIH-derived products to generate drought-resistant plants.

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.

Grain and Leaf Anthocyanin Concentration Varies among Purple Rice Varieties and Growing Condition in Aerated and Flooded Soil.

Anthocyanins are a group of pigments responsible for the red-blue color in plant parts, and have potential for health benefits and pharmaceutical ingredients. To evaluate whether anthocyanin concentrations in five purple rice varieties could be varied by water condition, plants were grown in waterlogged and aerobic (well-drained) soil. Grain anthocyanin concentration and grain yield were measured at maturity, while leaf anthocyanin concentrations were measured at booting and flowering stages. Four varieties grown under the waterlogged condition had 2.0−5.5 times higher grain anthocyanin than in the aerobic condition. There was a positive relationship between grain and leaf anthocyanin at booting in the waterlogged condition (r = 0.90, p < 0.05), while grain and leaf anthocyanin were positively correlated at flowering in both the waterlogged (r = 0.88, p < 0.05) and aerobic (r = 0.97, p < 0.01) conditions. The results suggest that water management should be adopted as a practical agronomic tool for improving the anthocyanin concentration of purple rice for specialist markets, but the specific responses between rice varieties to water management should be carefully considered.

Coordinated homeostasis of essential mineral nutrients: a focus on iron.

In plants, iron (Fe) transport and homeostasis are highly regulated processes. Fe deficiency or excess dramatically limits plant and algal productivity. Interestingly, complex and unexpected interconnections between Fe and various macro- and micronutrient homeostatic networks, supposedly maintaining general ionic equilibrium and balanced nutrition, are currently being uncovered. Although these interactions have profound consequences for our understanding of Fe homeostasis and its regulation, their molecular bases and biological significance remain poorly understood. Here, we review recent knowledge gained on how Fe interacts with micronutrient (e.g. zinc, manganese) and macronutrient (e.g. sulfur, phosphate) homeostasis, and on how these interactions affect Fe uptake and trafficking. Finally, we highlight the importance of developing an improved model of how Fe signaling pathways are integrated into functional networks to control plant growth and development in response to fluctuating environments.

GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways.

Plants need to cope with strong variations of nitrogen availability in the soil. Although many molecular players are being discovered concerning how plants perceive NO3- provision, it is less clear how plants recognize a lack of nitrogen. Following nitrogen removal, plants activate their nitrogen starvation response (NSR), which is characterized by the activation of very high-affinity nitrate transport systems (NRT2.4 and NRT2.5) and other sentinel genes involved in N remobilization such as GDH3. Using a combination of functional genomics via transcription factor perturbation and molecular physiology studies, we show that the transcription factors belonging to the HHO subfamily are important regulators of NSR through two potential mechanisms. First, HHOs directly repress the high-affinity nitrate transporters, NRT2.4 and NRT2.5. hho mutants display increased high-affinity nitrate transport activity, opening up promising perspectives for biotechnological applications. Second, we show that reactive oxygen species (ROS) are important to control NSR in wild-type plants and that HRS1 and HHO1 overexpressors and mutants are affected in their ROS content, defining a potential feed-forward branch of the signaling pathway. Taken together, our results define the relationships of two types of molecular players controlling the NSR, namely ROS and the HHO transcription factors. This work (i) up opens perspectives on a poorly understood nutrient-related signaling pathway and (ii) defines targets for molecular breeding of plants with enhanced NO3- uptake.

Plant resilience to phosphate limitation: current knowledge and future challenges.

Phosphorus (P) is an essential macronutrient for all living organisms. Importantly, plants require a large amount of P to grow, and P deficiency causes huge losses in plant production. Although this issue can be mitigated by the appropriate use of phosphate (Pi) rock-derived P fertilizers, phosphate rock is a finite natural resource. Moreover, the increased demand for food as a result of our growing global population is another factor contributing to a prospective P crisis. While creating crops that are resilient to Pi deficiency presents great scientific challenge, the current progress in our understanding of how plants regulate Pi homeostasis offers some opportunities for further study. In this review, we present the published research supporting these opportunities, which are based on the molecular mechanisms that plants have evolved to respond to P deficiency. First, we focus on recent advances in P sensing and signaling pathways in the regulation of root system architecture. Next, we describe the mechanisms that regulate Pi transport and accumulation, in a Pi- (or other nutrient) dependent manner. Integrating these data will help to design an innovative strategy for improving Pi nutrition in plants. In addition, this will help with Pi scarcity, one of the challenges facing agriculture in the twenty first century.

Natural allelic variation of the AZI1 gene controls root growth under zinc-limiting condition.

Zinc is an essential micronutrient for all living organisms and is involved in a plethora of processes including growth and development, and immunity. However, it is unknown if there is a common genetic and molecular basis underlying multiple facets of zinc function. Here we used natural variation in Arabidopsis thaliana to study the role of zinc in regulating growth. We identify allelic variation of the systemic immunity gene AZI1 as a key for determining root growth responses to low zinc conditions. We further demonstrate that this gene is important for modulating primary root length depending on the zinc and defence status. Finally, we show that the interaction of the immunity signal azelaic acid and zinc level to regulate root growth is conserved in rice. This work demonstrates that there is a common genetic and molecular basis for multiple zinc dependent processes and that nutrient cues can determine the balance of growth and immune responses in plants.

Integrative analysis of hexaploid wheat roots identifies signature components during iron starvation.

Iron (Fe) is an essential micronutrient for all organisms. In crop plants, Fe deficiency can decrease crop yield significantly; however, our current understanding of how major crops respond to Fe deficiency remains limited. Herein, the effect of Fe deprivation at both the transcriptomic and metabolic level in hexaploid wheat was investigated. Genome-wide gene expression reprogramming was observed in wheat roots subjected to Fe starvation, with a total of 5854 genes differentially expressed. Homoeologue and subgenome-specific analysis unveiled the induction-biased contribution from the A and B genomes. In general, the predominance of genes coding for nicotianamine synthase, yellow stripe-like transporters, metal transporters, ABC transporters, and zinc-induced facilitator-like protein was noted. Expression of genes related to the Strategy II mode of Fe uptake was also predominant. Our transcriptomic data were in agreement with the GC-MS analysis that showed the enhanced accumulation of various metabolites such as fumarate, malonate, succinate, and xylofuranose, which could be contributing to Fe mobilization. Interestingly, Fe starvation leads to a significant temporal increase of glutathione S-transferase at both the transcriptional level and enzymatic activity level, which indicates the involvement of glutathione in response to Fe stress in wheat roots. Taken together, our result provides new insight into the wheat response to Fe starvation at the molecular level and lays the foundation to design new strategies for the improvement of Fe nutrition in crops.

Improving phosphorus use efficiency: a complex trait with emerging opportunities.

Phosphorus (P) is one of the essential nutrients for plants, and is indispensable for plant growth and development. P deficiency severely limits crop yield, and regular fertilizer applications are required to obtain high yields and to prevent soil degradation. To access P from the soil, plants have evolved high- and low-affinity Pi transporters and the ability to induce root architectural changes to forage P. Also, adjustments of numerous cellular processes are triggered by the P starvation response, a tightly regulated process in plants. With the increasing demand for food as a result of a growing population, the demand for P fertilizer is steadily increasing. Given the high costs of fertilizers and in light of the fact that phosphate rock, the source of P fertilizer, is a finite natural resource, there is a need to enhance P fertilizer use efficiency in agricultural systems and to develop plants with enhanced Pi uptake and internal P-use efficiency (PUE). In this review we will provide an overview of continuing relevant research and highlight different approaches towards developing crops with enhanced PUE. In this context, we will summarize our current understanding of root responses to low phosphorus conditions and will emphasize the importance of combining PUE with tolerance of other stresses, such as aluminum toxicity. Of the many genes associated with Pi deficiency, this review will focus on those that hold promise or are already at an advanced stage of testing (OsPSTOL1, AVP1, PHO1 and OsPHT1;6). Finally, an update is provided on the progress made exploring alternative technologies, such as phosphite fertilizer.

TransDetect Identifies a New Regulatory Module Controlling Phosphate Accumulation.

Identifying transcription factor (TFs) cooperation controlling target gene expression is still an arduous challenge. The accuracy of current methods at genome scale significantly drops with the increase in number of genes, which limits their applicability to more complex genomes, like animals and plants. Here, we developed an algorithm, TransDetect, able to predict TF combinations controlling the expression level of a given gene. TransDetect was used to identify novel TF modules regulating the expression of Arabidopsis (Arabidopsis thaliana) phosphate transporter PHO1;H3 comprising MYB15, MYB84, bHLH35, and ICE1. These TFs were confirmed to interact between themselves and with the PHO1;H3 promoter. Phenotypic and genetic analyses of TF mutants enable the organization of these four TFs and PHO1;H3 in a new gene regulatory network controlling phosphate accumulation in zinc-dependent manner. This demonstrates the potential of TransDetect to extract directionality in nondynamic transcriptomes and to provide a blueprint to identify gene regulatory network involved in a given biological process.