Perfluorooctanesulfonic Acid Alters the Plant's Phosphate Transport Gene Network and Exhibits Antagonistic Effects on the Phosphate Uptake

Per- and polyfluoroalkyl substances (PFASs), with significant health risks to humans and wildlife, bioaccumulate in plants. However, the mechanisms underlying plant uptake remain poorly understood. This study deployed transcriptomic analysis coupled with genetic and physiological studies using Arabidopsis to investigate how plants respond to perfluorooctanesulfonic acid (PFOS), a long-chain PFAS. We observed increased expressions of genes involved in plant uptake and transport of phosphorus, an essential plant nutrient, suggesting intertwined uptake and transport processes of phosphorus and PFOS. Furthermore, PFOS-altered response differed from the phosphorus deficiency response, disrupting phosphorus metabolism to increase phosphate transporter (PHT) transcript. Interestingly, pht1;2 and pht1;8 mutants showed reduced sensitivity to PFOS compared to that of the wild type, implying an important role of phosphate transporters in PFOS sensing. Furthermore, PFOS accumulated less in the shoots of the pht1;8 mutant, indicating the involvement of PHT1;8 protein in translocating PFOS from roots to shoots. Supplementing phosphate improved plant's tolerance to PFOS and reduced PFOS uptake, suggesting that manipulating the phosphate source in PFOS-contaminated soils may be a promising strategy for minimizing PFOS uptake by edible crops or promoting PFOS uptake during phytoremediation. This study highlighted the critical role of phosphate sensing and transport system in the uptake and translocation of PFOS in plants.

SUMOylation of OsPSTOL1 is essential for regulating phosphate starvation responses in rice and Arabidopsis

Although rice is one of the main sources of calories for most of the world, nearly 60% of rice is grown in soils that are low in phosphorus especially in Asia and Africa. Given the limitations of bioavailable inorganic phosphate (Pi) in soils, it is important to develop crops tolerant to low phosphate in order to boost food security. Due to the immobile nature of Pi, plants have developed complex molecular signalling pathways that allow them to discern changes in Pi concentrations in the environment and adapt their growth and development. Recently, in rice, it was shown that a specific serine-threonine kinase known as Phosphorus-starvation tolerance 1 (PSTOL1) is important for conferring low phosphate tolerance in rice. Nonetheless, knowledge about the mechanism underpinning PSTOL1 activity in conferring low Pi tolerance is very limited in rice. Post-translation modifications (PTMs) play an important role in plants in providing a conduit to detect changes in the environment and influence molecular signalling pathways to adapt growth and development. In recent years, the PTM SUMOylation has been shown to be critical for plant growth and development. It is known that plants experience hyperSUMOylation of target proteins during phosphate starvation. Here, we demonstrate that PSTOL1 is SUMOylated in planta, and this affects its phosphorylation activity. Furthermore, we also provide new evidence for the role of SUMOylation in regulating PSTOL1 activity in plant responses to Pi starvation in rice and Arabidopsis. Our data indicated that overexpression of the non-SUMOylatable version of OsPSTOL1 negatively impacts total root length and total root surface area of rice grown under low Pi. Interestingly, our data also showed that overexpression of OsPSTOL1 in a non-cereal species, Arabidopsis, also positively impacts overall plant growth under low Pi by modulating root development. Taken together our data provide new evidence for the role of PSTOL1 SUMOylation in mediating enhanced root development for tolerating phosphate-limiting conditions.

Unraveling the potential of the strigolactones-NSP1/NSP2 friendship in crop improvement

Strigolactones (SLs) are fundamental to the ability of plants to cope with phosphate deficiency. A recent study by Yuan et al. indicates that the genetic module PHR2/NSP1/NSP2 is crucial in activating SL biosynthesis and signaling under inorganic phosphate (Pi) deficiency. Furthermore, this genetic module is essential for improving Pi and nitrogen homeostasis in rice.

Non-specific phospholipase C4 hydrolyzes phosphosphingolipids and phosphoglycerolipids and promotes rapeseed growth and yield

Phosphorus is a major nutrient vital for plant growth and development, with a substantial amount of cellular phosphorus being used for the biosynthesis of membrane phospholipids. Here, we report that NON-SPECIFIC PHOSPHOLIPASE C4 (NPC4) in rapeseed (Brassica napus) releases phosphate from phospholipids to promote growth and seed yield, as plants with altered NPC4 levels showed significant changes in seed production under different phosphate conditions. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated knockout of BnaNPC4 led to elevated accumulation of phospholipids and decreased growth, whereas overexpression (OE) of BnaNPC4 resulted in lower phospholipid contents and increased plant growth and seed production. We demonstrate that BnaNPC4 hydrolyzes phosphosphingolipids and phosphoglycerolipids in vitro, and plants with altered BnaNPC4 function displayed changes in their sphingolipid and glycerolipid contents in roots, with a greater change in glycerolipids than sphingolipids in leaves, particularly under phosphate deficiency conditions. In addition, BnaNPC4-OE plants led to the upregulation of genes involved in lipid metabolism, phosphate release, and phosphate transport and an increase in free inorganic phosphate in leaves. These results indicate that BnaNPC4 hydrolyzes phosphosphingolipids and phosphoglycerolipids in rapeseed to enhance phosphate release from membrane phospholipids and promote growth and seed production.

Recent Updates on ALMT Transporters' Physiology, Regulation, and Molecular Evolution in Plants

Aluminium toxicity and phosphorus deficiency in soils are the main interconnected problems of modern agriculture. The aluminium-activated malate transporters (ALMTs) comprise a membrane protein family that demonstrates various physiological functions in plants, such as tolerance to environmental Al3+ and the regulation of stomatal movement. Over the past few decades, the regulation of ALMT family proteins has been intensively studied. In this review, we summarise the current knowledge about this transporter family and assess their involvement in diverse physiological processes and comprehensive regulatory mechanisms. Furthermore, we have conducted a thorough bioinformatic analysis to decipher the functional importance of conserved residues, structural components, and domains. Our phylogenetic analysis has also provided new insights into the molecular evolution of ALMT family proteins, expanding their scope beyond the plant kingdom. Lastly, we have formulated several outstanding questions and research directions to further enhance our understanding of the fundamental role of ALMT proteins and to assess their physiological functions.

Carbon Fluxes in Potato (Solanum tuberosum) Remain Stable in Cell Cultures Exposed to Nutritional Phosphate Deficiency

Nutritional phosphate deficiency is a major limitation to plant growth. Here, we monitored fluxes in pathways supporting respiratory metabolism in potato (Solanum tuberosum) cell cultures growing in control or limiting phosphate conditions. Sugar uptake was quantified using [U-14C]sucrose as precursor. Carbohydrate degradation through glycolysis and respiratory pathways was estimated using the catabolism of [U-14C]sucrose to 14CO2. Anaplerotic carbon flux was assessed by labeling with NaH14CO3. The data showed that these metabolic fluxes displayed distinct patterns over culture time. However, phosphate depletion had relatively little impact on the various fluxes. Sucrose uptake was higher during the first six days of culture, followed by a decline, which was steeper in Pi-sufficient cells. Anaplerotic pathway flux was more important at day three and decreased thereafter. In contrast, the flux between sucrose and CO2 was at a maximum in the mid-log phase of the culture, with a peak at Day 6. Metabolization of [U-14C]sucrose into neutral, basic and acidic fractions was also unaffected by phosphate nutrition. Hence, the well-documented changes in central metabolism enzymes activities in response to Pi deficiency do not drastically modify metabolic fluxes, but rather result in the maintenance of the carbon fluxes that support respiration.

Evidence that a common arbuscular mycorrhizal network alleviates phosphate shortage in interconnected walnut sapling and maize plants

Under agroforestry practices, inter-specific facilitation between tree rows and cultivated alleys occurs when plants increase the growth of their neighbors especially under nutrient limitation. Owing to a coarse root architecture limiting soil inorganic phosphate (Pi) uptake, walnut trees (Juglans spp.) exhibit dependency on soil-borne symbiotic arbuscular mycorrhizal fungi that extend extra-radical hyphae beyond the root Pi depletion zone. To investigate the benefits of mycorrhizal walnuts in alley cropping, we experimentally simulated an agroforestry system in which walnut rootstocks RX1 (J. regia x J. microcarpa) were connected or not by a common mycelial network (CMN) to maize plants grown under two contrasting Pi levels. Mycorrhizal colonization parameters showed that the inoculum reservoir formed by inoculated walnut donor saplings allowed the mycorrhization of maize recipient roots. Relative to non-mycorrhizal plants and whatever the Pi supply, CMN enabled walnut saplings to access maize Pi fertilization residues according to significant increases in biomass, stem diameter, and expression of JrPHT1;1 and JrPHT1;2, two mycorrhiza-inducible phosphate transporter candidates here identified by phylogenic inference of orthologs. In the lowest Pi supply, stem height, leaf Pi concentration, and biomass of RX1 were significantly higher than in non-mycorrhizal controls, showing that mycorrhizal connections between walnut and maize roots alleviated Pi deficiency in the mycorrhizal RX1 donor plant. Under Pi limitation, maize recipient plants also benefited from mycorrhization relative to controls, as inferred from larger stem diameter and height, biomass, leaf number, N content, and Pi concentration. Mycorrhization-induced Pi uptake generated a higher carbon cost for donor walnut plants than for maize plants by increasing walnut plant photosynthesis to provide the AM fungus with carbon assimilate. Here, we show that CMN alleviates Pi deficiency in co-cultivated walnut and maize plants, and may therefore contribute to limit the use of chemical P fertilizers in agroforestry systems.

ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses

Participating in both biotic and abiotic stress responses, plant-specific class III peroxidases (PERs) show promise as candidates for crop improvement. The multigenic PER family is known to take part in diverse functions, such as lignin formation and defense against pathogens. Traditionally linked to hydrogen peroxide (H₂O₂) consumption, PERs can also produce reactive oxygen species (ROS), essential in tissue development, pathogen defense and stress signaling. The amino acid sequences of both orthologues and paralogues of PERs are highly conserved, but discovering correlations between sequence differences and their functional diversity has proven difficult. By combining meta-analysis of transcriptomic data and sequence alignments, we discovered a correlation between three key amino acid positions and gene expression in response to biotic and abiotic stresses. Phylogenetic analysis revealed evolutionary pressure on these amino acids toward stress responsiveness. Using AlphaFold modeling, we found unique interdomain and protein-heme interactions involving those key amino acids in stress-induced PERs. Plausibly, these structural interactions may act as "gate keepers" by preventing larger substrates from accessing the heme and thereby shifting PER function from consumption to the production of ROS.

Brassinosteroid signaling regulates phosphate starvation-induced malate secretion in plants

Inorganic phosphate (Pi) is often limited in soils due to precipitation with iron (Fe) and aluminum (Al). To scavenge heterogeneously distributed phosphorus (P) resources, plants have evolved a local Pi signaling pathway that induces malate secretion to solubilize the occluded Fe-P or Al-P oxides. In this study, we show that Pi limitation impaired brassinosteroid signaling and downregulated BRASSINAZOLE-RESISTANT 1 (BZR1) expression in Arabidopsis thaliana. Exogenous 2,4-epibrassinolide treatment or constitutive activation of BZR1 (in the bzr1-D mutant) significantly reduced primary root growth inhibition under Pi-starvation conditions by downregulating ALUMINUM-ACTIVATED MALATE TRANSPORTER 1 (ALMT1) expression and malate secretion. Furthermore, AtBZR1 competitively suppressed the activator effect of SENSITIVITY TO PROTON RHIZOTOXICITY 1 (STOP1) on ALMT1 expression and malate secretion in Nicotiana benthamiana leaves and Arabidopsis. The ratio of nuclear-localized STOP1 and BZR1 determined ALMT1 expression and malate secretion in Arabidopsis. In addition, BZR1-inhibited malate secretion is conserved in rice (Oryza sativa). Our findings provide insight into plant mechanisms for optimizing the secretion of malate, an important carbon resource, to adapt to Pi-deficiency stress.

Brassinosteroid signaling regulates phosphate starvation-induced malate secretion in plants

Inorganic phosphate (Pi) is often limited in soils due to precipitation with iron (Fe) and aluminum (Al). To scavenge heterogeneously distributed phosphorus (P) resources, plants have evolved a local Pi signaling pathway that induces malate secretion to solubilize the occluded Fe-P or Al-P oxides. In this study, we show that Pi limitation impaired brassinosteroid signaling and downregulated BRASSINAZOLE-RESISTANT 1 (BZR1) expression in Arabidopsis thaliana. Exogenous 2,4-epibrassinolide treatment or constitutive activation of BZR1 (in the bzr1-D mutant) significantly reduced primary root growth inhibition under Pi-starvation conditions by downregulating ALUMINUM-ACTIVATED MALATE TRANSPORTER 1 (ALMT1) expression and malate secretion. Furthermore, AtBZR1 competitively suppressed the activator effect of SENSITIVITY TO PROTON RHIZOTOXICITY 1 (STOP1) on ALMT1 expression and malate secretion in Nicotiana benthamiana leaves and Arabidopsis. The ratio of nuclear-localized STOP1 and BZR1 determined ALMT1 expression and malate secretion in Arabidopsis. In addition, BZR1-inhibited malate secretion is conserved in rice (Oryza sativa). Our findings provide insight into plant mechanisms for optimizing the secretion of malate, an important carbon resource, to adapt to Pi-deficiency stress.

Integrated multi-omics reveals the molecular mechanisms underlying efficient phosphorus use under phosphate deficiency in elephant grass (Pennisetum purpureum)

Phosphorus (P) is an essential macronutrient element for plant growth, and deficiency of inorganic phosphate (Pi) limits plant growth and yield. Elephant grass (Pennisetum purpureum) is an important fodder crop cultivated widely in tropical and subtropical areas throughout the world. However, the mechanisms underlying efficient P use in elephant grass under Pi deficiency remain poorly understood. In this study, the physiological and molecular responses of elephant grass leaves and roots to Pi deficiency were investigated. The results showed that dry weight, total P concentration, and P content decreased in Pi-deprived plants, but that acid phosphatase activity and P utilization efficiency (PUE) were higher than in Pi-sufficient plants. Regarding Pi starvation-responsive (PSR) genes, transcriptomics showed that 59 unigenes involved in Pi acquisition and transport (especially 18 purple acid phosphatase and 27 phosphate transporter 1 unigenes) and 51 phospholipase unigenes involved in phospholipids degradation or Pi-free lipids biosynthesis, as well as 47 core unigenes involved in the synthesis of phenylpropanoids and flavonoids, were significantly up-regulated by Pi deprivation in leaves or roots. Furthermore, 43 unigenes related to Pi-independent- or inorganic pyrophosphate (PPi)-dependent bypass reactions were markedly up-regulated in Pi-deficient leaves, especially five UDP-glucose pyrophosphorylase and 15 phosphoenolpyruvate carboxylase unigenes. Consistent with PSR unigene expression changes, metabolomics revealed that Pi deficiency significantly increased metabolites of Pi-free lipids, phenylpropanoids, and flavonoids in leaves and roots, but decreased phospholipid metabolites. This study reveals the mechanisms underlying the responses to Pi starvation in elephant grass leaves and roots, which provides candidate unigenes involved in efficient P use and theoretical references for the development of P-efficient elephant grass varieties.

Integrated mRNA and microRNA expression analysis of root response to phosphate deficiency in Medicago sativa

The deficiency of available phosphate significantly limits plant growth and development. This study sought to investigate how alfalfa (Medicago sativa), a high-yielding and high-quality forage widely cultivated worldwide, responds to phosphate deficiency stress by integrating transcriptional and post-transcriptional data. In this study, 6,041 differentially expressed genes (DEGs) were identified in alfalfa roots under phosphate deficiency conditions. Furthermore, psRNATarget, RNAhybrid, and TargetFinder were used to predict the target genes of 137 differentially expressed miRNAs (DEMs) in the root. In total, 3,912 DEGs were predicted as target genes. Pearson correlation analysis revealed 423 pairs of miRNA-mRNA regulatory relationships. MiRNA negatively regulates mRNA involved in regulatory pathways of phosphate deficiency responses in alfalfa. miR156e targeted squamosa promoter-binding-like protein 13A (SPL13), miR160c targeted auxin response factor 18 (ARF18), and miR2587a controlled glycolysis and citrate cycle via Phosphoenolpyruvate carboxykinase (ATP) (PCKA). Novel-miR27 regulated SPX domain-containing protein that controls phosphate transport in alfalfa root, novel-miR3-targeted sulfoquinovosyl transferase SQD2 controlled sulfolipid synthesis and glutathione S-transferase (GST; mediated by miR169j/k and novel-miR159) regulated glutathione metabolism. miR399l regulated auxin-responsive protein SAUR72 involved in IAA signal transduction, while abscisic acid receptor PYL4 (regulated by novel-miR205 and novel-miR83) participated in ABA signal transduction. Combined miRNA-mRNA enrichment analysis showed that most miRNAs regulate the phosphate starvation response of alfalfa by modulating target genes involved in carbohydrate metabolism, sulfolipid metabolism, glutathione metabolism, and hormone signal transduction. Therefore, this study provides new insights into the post-transcriptional regulation mechanism of phosphate deficiency responses and new perspectives on phosphate assimilation pathways in alfalfa and other legumes.

The Root Hair Development of Pectin Polygalacturonase PGX2 Activation Tagging Line in Response to Phosphate Deficiency

Pectin, cellulose, and hemicellulose constitute the primary cell wall in eudicots and function in multiple developmental processes in plants. Root hairs are outgrowths of specialized epidermal cells that absorb water and nutrients from the soil. Cell wall architecture influences root hair development, but how cell wall remodeling might enable enhanced root hair formation in response to phosphate (P) deficiency remains relatively unclear. Here, we found that POLYGALACTURONASE INVOLVED IN EXPANSION 2 (PGX2) functions in conditional root hair development. Under low P conditions, a PGX2 activation tagged line (PGX2^AT ) displays bubble-like root hairs and abnormal callose deposition and superoxide accumulation in roots. We found that the polar localization and trafficking of PIN2 are altered in PGX2^AT roots in response to P deficiency. We also found that actin filaments were less compact but more stable in PGX2^AT root hair cells and that actin filament skewness in PGX2^AT root hairs was recovered by treatment with 1-N-naphthylphthalamic acid (NPA), an auxin transport inhibitor. These results demonstrate that activation tagging of PGX2 affects cell wall remodeling, auxin signaling, and actin microfilament orientation, which may cooperatively regulate root hair development in response to P starvation.

Research Advances in the Mutual Mechanisms Regulating Response of Plant Roots to Phosphate Deficiency and Aluminum Toxicity

Low phosphate (Pi) availability and high aluminum (Al) toxicity constitute two major plant mineral nutritional stressors that limit plant productivity on acidic soils. Advances toward the identification of genes and signaling networks that are involved in both stresses in model plants such as Arabidopsis thaliana and rice (Oryza sativa), and in other plants as well have revealed that some factors such as organic acids (OAs), cell wall properties, phytohormones, and iron (Fe) homeostasis are interconnected with each other. Moreover, OAs are involved in recruiting of many plant-growth-promoting bacteria that are able to secrete both OAs and phosphatases to increase Pi availability and decrease Al toxicity. In this review paper, we summarize these mutual mechanisms by which plants deal with both Al toxicity and P starvation, with emphasis on OA secretion regulation, plant-growth-promoting bacteria, transcription factors, transporters, hormones, and cell wall-related kinases in the context of root development and root system architecture remodeling that plays a determinant role in improving P use efficiency and Al resistance on acidic soils.

Effects of Root Zone Warming on Maize Seedling Growth and Photosynthetic Characteristics Under Different Phosphorus Levels

Phosphorus content and root zone temperature are two major environmental factors affecting maize growth. Both low phosphorus and root zone high temperature stress significantly affect the growth of maize, but the comprehensive effects of phosphorus deficiency and root zone warming are less studied. This study aimed to explore the effects of phosphorus deficiency and root zone warming on the root absorption capacity, total phosphorus content, and photosynthetic fluorescence parameters of maize seedlings. The results showed that maize shoots and roots had different responses to root zone warming and phosphorus deficiency. Properly increasing the root zone temperature was beneficial to the growth of maize seedlings, but when the root zone temperature was too high, it significantly affected the root and shoot development of maize seedlings. The root zone warming had a more significant impact on the root system, while phosphorus deficiency had a greater impact on the shoots. Phosphorus content and root zone warming had a strong interaction. Under the comprehensive influence of normal phosphorus supply and medium temperature in the root zone, the growth of maize seedlings was the best. Under the combined effects of low phosphorus and high temperature in the root zone, the growth was the worst. Compared with the combination of normal phosphorus and root zone medium temperature treatment, the dry mass of the low-phosphorus root zone high temperature treatment was decreased by 55.80%. Under the condition of low-phosphorus too high root zone temperature reduced root vitality, plant phosphorus content, which in turn affected plant growth and light energy utilization efficiency. In the case of sufficient phosphate fertilizer supply, appropriately increasing the soil temperature in the root zone is beneficial to increase the absorption and utilization of phosphorus by plants and promote the growth and development of maize seedlings.

Transcriptome Analysis of Zygophyllum xanthoxylum Adaptation Strategies to Phosphate Stress

Soil phosphate (Pi) deficiency is a global issue and a major constraint on plant growth. Plants typically acclimatize to low Pi by enhancing their P utilization and/or P acquisition efficiencies; however, different species have variable preferred strategies. RNA sequencing analysis was performed on the shoots and roots of Zygophyllum xanthoxylum, under 1 day and 10 days of Pi stress, to investigate their adaptation strategies to P deprivation. A total of 364,614 unigenes and 9,270 differentially expressed genes (DEGs) were obtained via transcriptome sequencing. An analysis of the DEGs revealed that under the 10D treatment, anthocyanin synthesis genes were upregulated under Pi stress, whereas gibberellin, ethylene, and cytokinins synthesis genes were upregulated, and abscisic acid synthesis genes were downregulated. Genes related to organic acid synthesis, encoding for purple acid phosphatases (APase) and nucleases (RNase) were upregulated under the 1D and 10D treatments, respectively. Furthermore, genes associated with Pi transport were induced by Pi stress. Zygophyllum xanthoxylum has special P adaptation strategies, the variation trends of genes involved in external P mobilization and acquisition, which were different from that of most other species; however, the expression levels of organophosphorus mobilization related genes, such as APases and RNases, were significantly increased. Meanwhile, PHT2s and TPTs, which distributed Pi to effective sites (e.g., chloroplast), played critical roles in the maintenance of photosynthesis. We speculated that these were economic and energy saving strategies, and there are critical adaptive mechanisms that Z. xanthoxylum employs to cope with deficits in Pi.

GTPase ROP6 negatively modulates phosphate deficiency through inhibition of PHT1;1 and PHT1;4 in Arabidopsis thaliana

Phosphorus, an essential macroelement for plant growth and development, is a major limiting factor for sustainable crop yield. The Rho of plant (ROP) GTPase is involved in regulating multiple signal transduction processes in plants, but potentially including the phosphate deficiency signaling pathway remains unknown. Here, we identified that the rop6 mutant exhibited a dramatic tolerant phenotype under Pi-deficient conditions, with higher phosphate accumulation and lower anthocyanin content. In contrast, the rop6 mutant was more sensitive to arsenate (As(V)) toxicity, the analog of Pi. Immunoblot analysis displayed that the ROP6 protein was rapidly degraded through ubiquitin/26S proteasome pathway under Pi-deficient conditions. In addition, pull-down assay using GST-RIC1 demonstrated that the ROP6 activity was decreased obviously under Pi-deficient conditions. Strikingly, protein-protein interaction and two-voltage clamping assays demonstrated that ROP6 physically interacted with and inhibited the key phosphate uptake transporters PHT1;1 and PHT1;4 in vitro and in vivo. Moreover, genetic analysis showed that ROP6 functioned upstream of PHT1;1 and PHT1;4. Thus, we conclude that GTPase ROP6 modulates the uptake of phosphate by inhibiting the activities of PHT1;1 and PHT1;4 in Arabidopsis.

Combined Transcriptome and Proteome Analysis of Maize (Zea mays L.) Reveals A Complementary Profile in Response to Phosphate Deficiency

A deficiency in the macronutrient phosphate (Pi) brings about various changes in plants at the morphological, physiological and molecular levels. However, the molecular mechanism for regulating Pi homeostasis in response to low-Pi remains poorly understood, particularly in maize (Zea mays L.), which is a staple crop and requires massive amounts of Pi. Therefore, in this study, we performed expression profiling of the shoots and roots of maize seedlings with Pi-tolerant genotype at both the transcriptomic and proteomic levels using RNA sequencing and isobaric tags for relative and absolute quantitation (iTRAQ). We identified 1944 differentially expressed transcripts and 340 differentially expressed proteins under low-Pi conditions. Most of the differentially expressed genes were clustered as regulators, such as transcription factors involved in the Pi signaling pathway at the transcript level. However, the more functional and metabolism-related genes showed expression changes at the protein level. Moreover, under low-Pi conditions, Pi transporters and phosphatases were specifically induced in the roots at both the transcript and protein levels, and increased amounts of mRNA and protein of two purple acid phosphatases (PAPs) and one UDP-sulfoquinovose synthase (SQD) were specifically detected in the roots. The new insights provided by this study will help to improve the P-utilization efficiency of maize.

Long-distance blue light signalling regulates phosphate deficiency-induced primary root growth inhibition

Although roots are mainly embedded in the soil, recent studies revealed that light regulates mineral nutrient uptake by roots. However, it remains unclear whether the change in root system architecture in response to different rhizosphere nutrient statuses involves light signaling. Here, we report that blue light regulates primary root growth inhibition under phosphate-deficient conditions through the cryptochromes and their downstream signaling factors. We showed that the inhibition of root elongation by low phosphate requires blue light signal perception at the shoot and transduction to the root. In this process, SPA1 and COP1 play a negative role while HY5 plays a positive role. Further experiments revealed that HY5 is able to migrate from the shoot to root and that the shoot-derived HY5 autoactivates root HY5 and regulates primary root growth by directly activating the expression of LPR1, a suppressor of root growth under phosphate starvation. Taken together, our study reveals a regulatory mechanism by which blue light signaling regulates phosphate deficiency-induced primary root growth inhibition, providing new insights into the crosstalk between light and nutrient signaling.

Transcription Factor WRKY33 Mediates the Phosphate Deficiency-Induced Remodeling of Root Architecture by Modulating Iron Homeostasis in Arabidopsis Roots

The remodeling of root architecture is regarded as a major development to improve the plant's adaptivity to phosphate (Pi)-deficient conditions. The WRKY transcription factors family has been reported to regulate the Pi-deficiency-induced systemic responses by affecting Pi absorption or transportation. Whether these transcription factors act as a regulator to mediate the Pi-deficiency-induced remodeling of root architecture, a typical local response, is still unclear. Here, we identified an Arabidopsis transcription factor, WRKY33, that acted as a negative regulator to mediate the Pi-deficiency-induced remodeling of root architecture. The disruption of WRKY33 in wrky33-2 mutant increased the plant's low Pi sensitivity by further inhibiting the primary root growth and promoting the formation of root hair. Furthermore, we revealed that WRKY33 negatively regulated the remodeling of root architecture by controlling the transcriptional expression of ALMT1 under Pi-deficient conditions, which further mediated the Fe³⁺ accumulation in root tips to inhibit the root growth. In conclusion, this study demonstrates a previously unrecognized signaling crosstalk between WRKY33 and the ALMT1-mediated malate transport system to regulate the Pi deficiency responses.

Co-Inoculation of Mesorhizobium ciceri with Either Bacillus sp. or Enterobacter aerogenes on Chickpea Improves Growth and Productivity in Phosphate-Deficient Soils in Dry Areas of a Mediterranean Region

Biological nitrogen fixation requires a large amount of phosphorus (P). However, most of the soils are P-deficient and the extensive use of P- chemical fertilizers constitute a serious threat to the environment. In this context, two field experiments were carried out to investigate the effect of co-inoculation of Mesorhizobium ciceri with phosphate solubilizing bacteria (PSB), Bacillus sp., and Enterobacter aerogenes, on chickpea as an alternative to chemical nitrogen (N) and phosphorous fertilizers in P-deficient soils in dry areas of Morocco. The results revealed that combined inoculation of chickpea with rhizobia and PSB showed a significant enhancement of chickpea nodulation, biomass production, yields and N, P, and protein content in grains as compared to single inoculation or single application of N or P. A significantly higher increase was obtained by inoculating chickpea with Mesorhizobium sp. MA72 combined with E. aerogenes P1S6. This combination allowed an enhancement of more than 270% in nodulation, 192% in shoot dry weight and 242% in grain yield. The effect of this combination was equivalent to the effect of combined application of N and P fertilizers. Formulation of biofertilizers based on tasted strains could be used for chickpea co-inoculation in P-deficient soils for an eco-friendly sustainable production of chickpea.

The Ca2+ -regulated protein kinase CIPK1 integrates plant responses to phosphate deficiency in Arabidopsis thaliana

Phosphate (Pi) deficiency severely restricts plant growth and development, as Pi is an essential macronutrient. Calcium (Ca²⁺ ) is a ubiquitous second messenger in plants; calcineurin B-like proteins (CBL) and CBL-interacting protein kinases (CIPK) are signalling pathways that act as an important Ca²⁺ signalling network which integrates plants to fine tune the response to stress; however, whether CIPK are involved in Pi deficiency stress remains largely unknown. In this study, we carried out a reverse genetic strategy to screen T-DNA insertion mutants of CIPK isoforms under Pi deficiency in Arabidopsis thaliana. Then Pi content, transcription of phosphate starvation-induced (PSI) genes, acid phosphatase activity and hydrogen peroxide were determined in the wild-type (WT) and cipk1 mutant, respectively. The phenotype of CIPK1 complementation lines was analysed. The cipk1 mutant had a more sensitive phenotype, with lower root elongation and root length, and decreased Pi content compared with the WT under Pi deficiency. Moreover, CIPK1 mutation caused phosphate starvation-induced (PSI) genes to be significantly induced under Pi deficiency. Histological staining demonstrated that the cipk1 mutant had increased acid phosphatase activity and hydrogen peroxide concentration under Pi deficiency. By using the yeast two-hybrid system, we further demonstrated the interaction between CIPK1 and the WRKY transcription factors, WRKY6 and WRKY42. Overall, we demonstrate that CIPK1 is involved in the Pi deficiency signalling pathway in A. thaliana, revealing the important role of Ca²⁺ in the Pi nutrition signalling pathway, and potentially providing a theoretical foundation for molecular breeding of crops with better Pi utilization efficiency.

Strigolactones Decrease Leaf Angle in Response to Nutrient Deficiencies in Rice

Strigolactones (SLs) are a class of plant hormones that are synthesized from β-carotene through sequential reactions catalyzed by DWARF (D) 27, D17, D10, and OsMORE AXILLARY GROWTH (MAX) 1 in rice (Oryza sativa L.). In rice, endogenous SL levels increase in response to deficiency of nitrogen, phosphate, or sulfate (-N, -P, or -S). Rice SL mutants show increased lamina joint (LJ) angle as well as dwarfism, delayed leaf senescence, and enhanced shoot branching. The LJ angle is an important trait that determines plant architecture. To evaluate the effect of endogenous SLs on LJ angle in rice, we measured LJ angle and analyzed the expression of SL-biosynthesis genes under macronutrient deficiencies. In the "Shiokari" background, LJ angle was significantly larger in SL mutants than in the wild-type (WT). In WT and SL-biosynthesis mutants, direct treatment with the SL synthetic analog GR24 decreased the LJ angle. In WT, deficiency of N, P, or S, but not of K, Ca, Mg, or Fe decreased LJ angle. In SL mutants, deficiency of N, P, or S had no such effect. We analyzed the time course of SL-related gene expression in the LJ of WT deficient in N, P, or S, and found that expression of SL-biosynthesis genes increased 2 or 3 days after the onset of deficiency. Expression levels of both the SL-biosynthesis and signaling genes was particularly strongly increased under -P. Rice cultivars "Nipponbare", "Norin 8", and "Kasalath" had larger LJ angle than "Shiokari", interestingly with no significant differences between WT and SL mutants. In "Nipponbare", endogenous SL levels increased and the LJ angle was decreased under -N and -P. These results indicate that SL levels increased in response to nutrient deficiencies, and that elevated endogenous SLs might negatively regulate leaf angle in rice.

Low phosphate represses histone deacetylase complex1 to regulate root system architecture remodeling in Arabidopsis

The mechanisms involved in the regulation of gene expression in response to phosphate (Pi) deficiency have been extensively studied, but their chromatin-level regulation remains poorly understood. We examined the role of histone acetylation in response to Pi deficiency by using the histone deacetylase complex1 (hdc1) mutant. Genes involved in root system architecture (RSA) remodeling were analyzed by quantitative real-time polymerase chain reaction (qPCR) and chromatin immunoprecipitation qPCR. We demonstrate that histone H3 acetylation increased under Pi deficiency, and the hdc1 mutant was hypersensitive to Pi deficiency, with primary root growth inhibition and increases in root hair number. Concomitantly, Pi deficiency repressed HDC1 protein abundances. Under Pi deficiency, hdc1 accumulated higher concentrations of Fe³⁺ in the root tips and had higher expression of genes involved in RSA remodeling, such as ALUMINUM-ACTIVATED MALATE TRANSPORTER1 (ALMT1), LOW PHOSPHATE ROOT1 (LPR1), and LPR2 compared with wild-type plants. Furthermore, Pi deficiency enriched the histone H3 acetylation of ALMT1 and LPR1. Finally, genetic evidence showed that LPR1/2 was epistatic to HDC1 in regulating RSA remodeling. Our results suggest a chromatin-level control of Pi starvation responses in which HDC1-mediated histone H3 deacetylation represses the transcriptional activation of genes involved in RSA remodeling in Arabidopsis.

(Poly)phenols, Carotenoids, and Tocochromanols in Corn (Zea mays L.) Kernels As Affected by Phosphate Fertilization and Sowing Time

Corn (Zea mays L.) growth and development is often limited by the availability of phosphate. We thus hypothesized that phosphate fertilization may increase the contents of (poly)phenols, carotenoids, and tocochromanols (vitamin E) in corn grains. Corn plants cultivated on a soil fertilized with 44 kg phosphorus/ha were compared to plants grown on soil with low plant-available phosphate (1.6 mg CAL-P/100 g of soil), each sown early (April) and late (May) in a randomized field experiment. HPLC-DAD-(HR)-ESI-MSⁿ revealed 19 soluble and 10 insoluble (poly)phenols, comprising phenolic acids, phenolic amines, diferulic, and triferulic acids in corn grains. Contents of individual (poly)phenols, carotenoids, and tocochromanols in whole grains were significantly (p < 0.05) increased by sowing time, but not by phosphate fertilization. In conclusion, low phosphate availability did not impair the biosynthesis of (poly)phenols, carotenoids, and tocochromanols in corn grains.

Do Phosphate and Cytokinin Interact to Regulate Strigolactone Biosynthesis or Act Independently?

Strigolactones (SLs) are essential host recognition signals for both root-parasitic plants and arbuscular mycorrhizal (AM) fungi in the rhizosphere, and in planta SLs or their metabolites function as a novel class of plant hormones that regulate various aspects of plant growth through crosstalk with other hormones. Although nutrient availability is one of the important factors influencing SL production and exudation, and phosphate (Pi) deficiency significantly promotes SL production and exudation in host plants of AM fungi, how nutrient availability modulates SL production and exudation remains elusive. Cytokinin (CK), a canonical plant hormone, has extensively been studied as a shoot branching promoter and its biosynthesis is also influenced by mineral nutrients, especially nitrate, indicating that CK might be another key factor that affect SL production and exudation. In the present study, we show that CKs (t-zeatin, benzyladenine, kinetin, and CPPU) applied to hydroponic culture media significantly suppressed the SL levels in both the root exudates and the root tissues of rice plants grown under Pi deficiency. In a split-root system, CK suppressed SL production locally, while Pi affected SL production systemically, suggesting that Pi and CK act on SL production independently in rice plants.

Blue Light-Triggered Chemical Reactions Underlie Phosphate Deficiency-Induced Inhibition of Root Elongation of Arabidopsis Seedlings Grown in Petri Dishes

To tolerate phosphate (Pi) deficiency in the environment, plants alter their developmental and metabolic programs. In the past two decades, researchers have extensively used Petri dish-grown seedlings of the model plant Arabidopsis thaliana to study the molecular mechanisms underlying root developmental responses to Pi deficiency. A typical developmental response of the Petri dish-grown Arabidopsis seedlings to Pi deficiency is the inhibited growth of primary root (PR). This response is generally thought to enhance the production of lateral roots and root hairs, which increases the plant's ability to obtain Pi and is therefore regarded as an active cellular response. Here, we report that direct illumination of root surface with blue light is critical and sufficient for Pi deficiency-induced inhibition of PR growth in Arabidopsis seedlings. We further show that a blue light-triggered malate-mediated photo-Fenton reaction and a canonical Fenton reaction form an Fe redox cycle in the root apoplast. This Fe redox cycle results in the production of hydroxyl radicals that inhibit PR growth. In addition to revealing the molecular mechanism underlying Pi deficiency-induced inhibition of PR growth, our work demonstrated that this developmental change is not an active cellular response; instead, it is a phenotype resulting from root growth in transparent Petri dishes. This finding is significant because illuminated, transparent Petri dishes have been routinely used to study Arabidopsis root responses to environmental changes.

Phosphorus Limitation Improved Salt Tolerance in Maize Through Tissue Mass Density Increase, Osmolytes Accumulation, and Na+ Uptake Inhibition

Low phosphorus (P) availability and salt stress are two major constraints for maize (Zea mays L.) growth in north China. A combination of salinity and high P rather than low P is more detrimental to the growth of maize. However, little is known about the mechanisms by which P nutrition modifies the salt tolerance and P uptake of maize. The present study aimed to investigate the combined effects of salinity and P on maize growth and P uptake, and to address the physiological mechanisms of salt tolerance influenced by P availability in maize. Seedlings of a local maize cultivar XY335 were grown hydroponically for 35 days under low (5 μM) or sufficient P supply (200 μM) with or without 100 mM NaCl. Root morphological traits, tissue mass density, leaf osmolytes (sugars and proline) accumulation, and Na+/K+ ratio were measured to allow evaluation of the combined effects of salinity and P on maize growth and P uptake. Both P deficiency and salinity markedly reduced the growth of maize. However, P deficiency had a more pronounced effect on shoot growth while salinity affected root growth more prominently. Combined effects of P deficiency and salinity on total root length, root surface area, and average root diameter were similar to that of plants grown under salt stress. The combination of P deficiency and salinity treatments had a more pronounced effect on tissue mass density, leaf proline and soluble sugars compared to individual treatment of either low P or NaCl. When exposed to salt stress, maize plants of sufficient P accumulated greater amount of Na+ than those under P deficit, but similar amounts of K+ were observed between the two P treatments. Salt stress significantly increased shoot P concentration of maize with sufficient P (P < 0.01), but not for P-deficient plants. In sum, shoots and roots of maize exhibited different responses to P deficiency and salinity, with more marked effect of P deficiency on shoots and of salinity on roots. P deficiency improved salt tolerance of maize plants, which was associated with the increase of tissue mass density, accumulation of osmolytes, reduction of Na+ accumulation, and selective absorption of K+ over Na+.

Editing of the OsACS locus alters phosphate deficiency-induced adaptive responses in rice seedlings

Phosphate (Pi) deficiency severely influences the growth and reproduction of plants. To cope with Pi deficiency, plants initiate morphological and biochemical adaptive responses upon sensing low Pi in the soil, and the plant hormone ethylene plays a crucial role during this process. However, how regulation of ethylene biosynthesis influences the Pi-induced adaptive responses remains unclear. Here, we determine the roles of rice 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS), the rate-limiting enzymes in ethylene biosynthesis, in response to Pi deficiency. Through analysis of tissue-specific expression of OsACS in response to Pi deficiency and OsACS mutants generated by CRISPR/Cas9 [clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9] genome editing, we found that two members of the OsACS family, i.e. OsACS1 and OsACS2, are involved but differed in their importance in controlling the remodeling of root system architecture, transcriptional regulation of Pi starvation-induced genes, and cellular phosphorus homeostasis. Interestingly, in contrast to the known inhibitory role of ethylene on root elongation, both OsACS mutants, especially OsACS1, almost fail to promote lateral root growth in response to Pi deficiency, demonstrating a stimulatory role for ethylene in lateral root development under Pi-deficient conditions. Together, this study provides new insights into the roles of ethylene in Pi deficiency response in rice seedlings and the isoform-specific function of OsACS genes in this process.

Blue Light Regulates Phosphate Deficiency-Dependent Primary Root Growth Inhibition in Arabidopsis

Plants have evolved mechanisms to improve utilization efficiency or acquisition of inorganic phosphate (Pi) in response to Pi deficiency, such as altering root architecture, secreting acid phosphatases, and activating the expression of genes related to Pi uptake and recycling. Although many genes responsive to Pi starvation have been identified, transcription factors that affect tolerance to Pi deficiency have not been well characterized. We show here that the ectopic expression of B-BOX32 (BBX32) and the mutation of ELONGATED HYPOCOTYL 5 (HY5), whose transcriptional activity is negatively regulated by BBX32, resulted in the tolerance to Pi deficiency in Arabidopsis. The primary root lengths of 35S:BBX32 and hy5 plants were only slightly inhibited under Pi deficient condition and the fresh weights were significantly higher than those of wild type. The Pi deficiency-tolerant root phenotype of hy5 was similarly observed when grown on the medium without Pi. In addition, a double mutant, hy5 slr1, without lateral roots, also showed a long primary root phenotype under phosphate deficiency, indicating that the root phenotype of hy5 does not result from an increase of external Pi uptake. Moreover, we found that blue light may regulate Pi deficiency-dependent primary root growth inhibition through activating peroxidase gene expression, suggesting the Pi-deficiency tolerant root phenotype of hy5 may be due to blockage of blue light responses. Altogether, this study points out light quality may play an important role in the regulation of Pi deficiency responses. It may contribute to regulate plant growth under Pi deficiency through proper illumination.

Iron and Phosphate Deficiency Regulators Concertedly Control Coumarin Profiles in Arabidopsis thaliana Roots During Iron, Phosphate, and Combined Deficiencies

Plants face varying nutrient conditions, to which they have to adapt to. Adaptive responses are nutrient-specific and strategies to ensure supply and homeostasis for one nutrient might be opposite to another one, as shown for phosphate (P_i) and iron (Fe) deficiency responses, where many genes are regulated in an opposing manner. This was also observed on the metabolite levels. Whereas root and exudate levels of catechol-type coumarins, phenylpropanoid-derived 2-benzopyranones, which facilitate Fe acquisition, are elevated after Fe deficiency, they are decreased after P_i deficiency. Exposing plants to combined P_i and Fe deficiency showed that the generation of coumarin profiles in Arabidopsis thaliana roots by P_i deficiency considerably depends on the availability of Fe. Similarly, the effect of Fe deficiency on coumarin profiles is different at low compared to high P_i availability. These findings suggest a fine-tuning of coumarin profiles, which depends on Fe and P_i availability. T-DNA insertion lines exhibiting aberrant expression of genes involved in the regulation of P_i starvation responses (PHO1, PHR1, bHLH32, PHL1, SPX1) and Fe starvation responses (BRUTUS, PYE, bHLH104, FIT) were used to analyze the regulation of the generation of coumarin profiles in Arabidopsis thaliana roots by P_i, Fe, and combined P_i and Fe deficiency. The analysis revealed a role of several Fe-deficiency response regulators in the regulation of Fe and of P_i deficiency-induced coumarin profiles as well as for P_i deficiency response regulators in the regulation of P_i and of Fe deficiency-induced coumarin profiles. Additionally, the regulation of Fe deficiency-induced coumarin profiles by Fe deficiency response regulators is influenced by P_i availability. Conversely, regulation of P_i deficiency-induced coumarin profiles by P_i deficiency response regulators is modified by Fe availability.

Can Aluminum Tolerant Wheat Cultivar Perform Better under Phosphate Deficient Conditions?

Low availability of inorganic phosphate (Pi), together with aluminum (Al), is a major constraint for plant growth and development in acidic soils. To investigate whether or not Al-resistant cultivars can perform better under Pi deficiency, we chose two wheat cultivars with different Al-responses-Atlas 66, being Al-tolerant, and Scout 66, which is Al-sensitive-and analyzed their responses to Pi deficiency. Results showed that, unexpectedly, the Al-sensitive cultivar Scout 66 contained comparatively higher amount of soluble phosphate (Pi) and total phosphorus (P) both in the roots and in the shoots than Atlas 66 under P deficiency. In addition, Scout 66 exhibited higher root biomass, root volume, and root tip numbers, compared with Atlas 66. The expression of Pi-responsive marker genes, TaIPS1, TaSPX3, and TaSQD2 was strongly induced in both cultivars, but the extents of induction were higher in Scout 66 than in Atlas 66 under long-term Pi starvation. Taken together, our results suggest that the Al-sensitive cultivar Scout 66 performed much better under sole Pi starvation, which sets the following experimental stage to uncover the underlying mechanisms of why Scout 66 can display better under Pi deficiency. Our study also raises an open question whether Al-resistant plants are more sensitive to Pi deficiency.

Metabolomics and Transcriptomics in Legumes Under Phosphate Deficiency in Relation to Nitrogen Fixation by Root Nodules

Phosphate (Pi) deficiency is a critical environmental constraint that affects the growth and development of several legume crops that are usually cultivated in semi-arid regions and marginal areas. Pi deficiency is known to be a significant limitation for symbiotic nitrogen (N2) fixation (SNF), and variability in SNF is strongly interlinked with the concentrations of Pi in the nodules. To deal with Pi deficiency, plants trigger various adaptive responses, including the induction and secretion of acid phosphatases, maintenance of Pi homeostasis in nodules and other organs, and improvement of oxygen (O2) consumption per unit of nodule mass. These molecular and physiological responses can be observed in terms of changes in growth, photosynthesis, and respiration. In this mini review, we provide a brief introduction to the problem of Pi deficiency in legume crops. We then summarize the current understanding of how Pi deficiency is regulated in legumes by changes in the transcriptomes and metabolomes found in different plant organs. Finally, we will provide perspectives on future directions for research in this field.

Salvia castanea Hairy Roots are More Tolerant to Phosphate Deficiency than Salvia miltiorrhiza Hairy Roots Based on the Secondary Metabolism and Antioxidant Defenses

Salvia miltiorrhiza is a well-known traditional Chinese herb which is used to treat heart disease. Salvia castanea is a substitute product for S. miltiorrhiza in the medicinal field. Previous study has shown that phosphate (Pi) deficiency could promote the accumulation of secondary metabolism in herbs, and it has also developed a strategy for saving Pi resources and increasing the yield of active substances in herbs. In the present study, the hairy roots of S. miltiorrhiza and S. castanea were used to identify the Pi deficiency response mechanisms of these two Salvia species. The results showed that Pi deficiency increased the accumulation of specifically secondary metabolites, such as phenolic acids and tanshinones, which were caused by promoting the expression levels of key enzyme genes. In addition, Pi deficiency promoted the antioxidant activity in these two Salvia species. The data demonstrated that Pi deficiency increased the quality of the medicinal material in the plant. The hairy roots of S. castanea were more adaptive to Pi deficiency than those of S. miltiorrhiza in terms of biomass, secondary metabolism, and antioxidant activity. The results of this study provide insights into breeding herbs that are better adapted to Pi deficiency, which could increase the yield of active ingredients in herbs and save Pi resources.

Different effects of phospholipase Dζ2 and non-specific phospholipase C4 on lipid remodeling and root hair growth in Arabidopsis response to phosphate deficiency

Phosphate (Pi) deficiency in soils is a major limiting factor for plant growth. In response to Pi deprivation, one prominent metabolic adaptation in plants is the decrease in membrane phospholipids that consume approximately one-third cellular Pi. The level of two phospholipid-hydrolyzing enzymes, phospholipase Dζ2 (PLDζ2) and non-specific phospholipase C4 (NPC4), is highly induced in Pi-deprived Arabidopsis. To determine the role of PLDζ2 and NPC4 in plant growth under Pi limitation, Arabidopsis plants deficient in both PLDζ2 and NPC4 (npc4pldζ2) were generated and characterized. Lipid remodeling in leaves and roots was analyzed at three different durations of Pi deficiency. NPC4 affected lipid changes mainly in roots at an early stage of Pi deprivation, whereas PLDζ2 exhibited a more overt effect on lipid remodeling in leaves at a later stage of Pi deprivation. Pi deficiency-induced galactolipid increase and phospholipid decrease were impeded in pldζ2 and npc4pldζ2 plants. In addition, seedlings of npc4pldζ2 had the same root hair density as pldζ2 but shorter root hair length than pldζ2 in response to Pi deficiency. The loss of NPC4 decreased root hair length but had no effect on root hair density. These data suggest that PLDζ2 and NPC4 mediate the Pi deprivation-induced lipid remodeling in a tissue- and time-specific manner. PLDζ2 and NPC4 have distinctively different roles in root hair growth and development in response to Pi deprivation; PLDζ2 negatively modulates root hair density and length, whereas NPC4 promotes root hair elongation.

Cellular Patterning of Arabidopsis Roots Under Low Phosphate Conditions

Phosphorus is a crucial macronutrient for plants playing a critical role in many cellular signaling and energy cycling processes. In light of this, phosphorus acquisition efficiency is an important target trait for crop improvement, but it also provides an ecological adaptation for growth of plants in low nutrient environments. Increased root hair density has been shown to improve phosphorus uptake and plant health in a number of species. In several plant families, including Brassicaceae, root hair bearing cells are positioned on the epidermis according to their position in relation to cortex cells, with hair cells positioned in the cleft between two underlying cortex cells. Thus the number of cortex cells determines the number of epidermal cells in the root hair position. Previous research has associated phosphorus-limiting conditions with an increase in the number of cortex cell files in Arabidopsis thaliana roots, but they have not investigated the spatial or temporal domains in which these extra divisions occur or explored the consequences this has had on root hair formation. In this study, we use 3D reconstructions of root meristems to demonstrate that the radial anticlinal cell divisions seen under low phosphate are exclusive to the cortex. When grown on media containing replete levels of phosphorous, A. thaliana plants almost invariably show eight cortex cells; however when grown in phosphate limited conditions, seedlings develop up to 16 cortex cells (with 10-14 being the most typical). This results in a significant increase in the number of epidermal cells at hair forming positions. These radial anticlinal divisions occur within the initial cells and can be seen within 24 h of transfer of plants to low phosphorous conditions. We show that these changes in the underlying cortical cells feed into epidermal patterning by altering the regular spacing of root hairs.

Comparative Analysis of the Combined Effects of Different Water and Phosphate Levels on Growth and Biological Nitrogen Fixation of Nine Cowpea Varieties

Water deficit and phosphate (Pi) deficiency adversely affect growth and biological nitrogen fixation (BNF) of legume crops. In this study, we examined the impact of interaction between soil water conditions and available soil-Pi levels on growth, nodule development and BNF potential of nine cowpea varieties grown on dry savanna soils. In our experimental design, soils with different available soil-Pi levels, i.e., low, moderate, and high soil-Pi levels, collected from various farming fields were used to grow nine cowpea varieties under well-watered and water-deficit conditions. Significant and severe water deficit-damaging effects on BNF, nodulation, growth, levels of plant-nitrogen (N) and -phosphorus (P), as well as shoot relative water content and chlorophyll content of cowpea plants were observed. Under well-watered and high available soil-Pi conditions, cowpea varieties IT07K-304-9 and Dan'Ila exhibited significantly higher BNF potential and dry biomass, as well as plant-N and -P contents compared with other tested ones. Significant genotypic variations among the cowpeas were recorded under low available soil-Pi and water-deficit conditions in terms of the BNF potential. Principal component (PC) analysis revealed that varieties IT04K-339-1, IT07K-188-49, IT07K-304-9, and IT04K-405-5 were associated with PC1, which was better explained by performance for nodulation, plant biomass, plant-N, plant-P, and BNF potential under the combined stress of water deficit and Pi deficiency, thereby offering prospects for development of varieties with high growth and BNF traits that are adaptive to such stress conditions in the region. On another hand, variety Dan'Ila was significantly related to PC2 that was highly explained by the plant shoot/root ratio and chlorophyll content, suggesting the existence of physiological and morphological adjustments to cope with water deficit and Pi deficiency for this particular variety. Additionally, increases in soil-Pi availability led to significant reductions of water-deficit damage on dry biomass, plant-N and -P contents, and BNF potential of cowpea varieties. This finding suggests that integrated nutrient management strategies that allow farmers to access to Pi-based fertilizers may help reduce the damage of adverse water deficit and Pi deficiency caused to cowpea crop in the regions, where soils are predominantly Pi-deficient and drought-prone.

Novel phosphate deficiency-responsive long non-coding RNAs in the legume model plant Medicago truncatula

Emerging evidence indicates that long non-coding RNAs (lncRNAs) play important roles in the regulation of many biological processes. Inhibition of plant growth due to deficiency in soil inorganic phosphate (Pi) occurs widely across natural and agricultural ecosystems; however, we know little about the function of plant lncRNAs in response to Pi deficiency. To address this issue, we first identified 10 785 lncRNAs in the legume model species Medicago truncatula by sequencing eight strand-specific libraries. Out of these lncRNAs, 358 and 224 were responsive to Pi deficiency in the leaves and roots, respectively. We further predicted and classified the putative targets of those lncRNAs and the results revealed that they may be involved in the processes of signal transduction, energy synthesis, detoxification, and Pi transport. Finally, we functionally characterized three Phosphate Deficiency-Induced LncRNAs (PDILs) using their corresponding Tnt1 mutants. The results showed that PDIL1 suppressed degradation of MtPHO2, which encodes a ubiquitin-conjugating E2 enzyme regulated by miR399, while PDIL2 and PDIL3 directly regulated Pi transport at the transcriptional level. These findings demonstrate that PDILs can regulate Pi-deficiency signaling and Pi transport, highlighting the involvement of lncRNAs in the regulation of responses of plants to Pi deficiency.

Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation

Noncoding RNAs are an underexplored reservoir of regulatory molecules in eukaryotes. We analyzed the environmental response of roots to phosphorus (Pi) nutrition to understand how a change in availability of an essential element is managed. Pi availability influenced translational regulation mediated by small upstream ORFs on protein-coding mRNAs. Discovery, classification, and evaluation of long noncoding RNAs (lncRNAs) associated with translating ribosomes uncovered diverse new examples of translational regulation. These included Pi-regulated small peptide synthesis, ribosome-coupled phased small interfering RNA production, and the translational regulation of natural antisense RNAs and other regulatory RNAs. This study demonstrates that translational control contributes to the stability and activity of regulatory RNAs, providing an avenue for manipulation of traits.

Eukaryotic transcriptomes contain a major non–protein-coding component that includes precursors of small RNAs as well as long noncoding RNA (lncRNAs). Here, we utilized the mapping of ribosome footprints on RNAs to explore translational regulation of coding and noncoding RNAs in roots of Arabidopsis thaliana shifted from replete to deficient phosphorous (Pi) nutrition. Homodirectional changes in steady-state mRNA abundance and translation were observed for all but 265 annotated protein-coding genes. Of the translationally regulated mRNAs, 30% had one or more upstream ORF (uORF) that influenced the number of ribosomes on the principal protein-coding region. Nearly one-half of the 2,382 lncRNAs detected had ribosome footprints, including 56 with significantly altered translation under Pi-limited nutrition. The prediction of translated small ORFs (sORFs) by quantitation of translation termination and peptidic analysis identified lncRNAs that produce peptides, including several deeply evolutionarily conserved and significantly Pi-regulated lncRNAs. Furthermore, we discovered that natural antisense transcripts (NATs) frequently have actively translated sORFs, including five with low-Pi up-regulation that correlated with enhanced translation of the sense protein-coding mRNA. The data also confirmed translation of miRNA target mimics and lncRNAs that produce trans-acting or phased small-interfering RNA (tasiRNA/phasiRNAs). Mutational analyses of the positionally conserved sORF of TAS3a linked its translation with tasiRNA biogenesis. Altogether, this systematic analysis of ribosome-associated mRNAs and lncRNAs demonstrates that nutrient availability and translational regulation controls protein and small peptide-encoding mRNAs as well as a diverse cadre of regulatory RNAs.

Enhancement of cell wall protein SRPP expression during emergent root hair development in Arabidopsis

SRPP is a protein expressed in seeds and root hairs and is significantly induced in root hairs under phosphate (Pi)-deficient conditions. Root hairs in the knockout mutant srpp-1 display defects, i.e., suppression of cell growth and cell death. Here, we analyzed the expression profile of SRPP during cell elongation of root hairs and compared the transcript levels in several mutants with short root hairs. The mRNA level was increased in wild-type plants and decreased in mutants with short root hairs. Induction of SRPP expression by Pi starvation occurred one or two days later than induction of Pi-deficient sensitive genes, such as PHT1 and PHF1. These results indicate that the expression of SRPP is coordinated with root hair elongation. We hypothesize that SRPP is essential for structural robustness of the cell walls of root hairs.

Comparative transcriptome analysis of nodules of two Mesorhizobium-chickpea associations with differential symbiotic efficiency under phosphate deficiency

Phosphate (Pi) deficiency is known to be a major limitation for symbiotic nitrogen fixation (SNF), and hence legume crop productivity globally. However, very little information is available on the adaptive mechanisms, particularly in the important legume crop chickpea (Cicer arietinum L.), which enable nodules to respond to low-Pi availability. Thus, to elucidate these mechanisms in chickpea nodules at molecular level, we used an RNA sequencing approach to investigate transcriptomes of the nodules in Mesorhizobium mediterraneum SWRI9-(MmSWRI9)-chickpea and M. ciceri CP-31-(McCP-31)-chickpea associations under Pi-sufficient and Pi-deficient conditions, of which the McCP-31-chickpea association has a better SNF capacity than the MmSWRI9-chickpea association during Pi starvation. Our investigation revealed that more genes showed altered expression patterns in MmSWRI9-induced nodules than in McCP-31-induced nodules (540 vs. 225) under Pi deficiency, suggesting that the Pi-starvation-more-sensitive MmSWRI9-induced nodules required expression change in a larger number of genes to cope with low-Pi stress than the Pi-starvation-less-sensitive McCP-31-induced nodules. The functional classification of differentially expressed genes (DEGs) was examined to gain an understanding of how chickpea nodules respond to Pi starvation, caused by soil Pi deficiency. As a result, more DEGs involved in nodulation, detoxification, nutrient/ion transport, transcriptional factors, key metabolic pathways, Pi remobilization and signalling were found in Pi-starved MmSWRI9-induced nodules than in Pi-starved McCP-31-induced nodules. Our findings have enabled the identification of molecular processes that play important roles in the acclimation of nodules to Pi deficiency, ultimately leading to the development of Pi-efficient chickpea symbiotic associations suitable for Pi-deficient soils.

Temporal development of the barley leaf metabolic response to Pi limitation

The response of plants to P_i limitation involves interplay between root uptake of P_i , adjustment of resource allocation to different plant organs and increased metabolic P_i use efficiency. To identify potentially novel, early-responding, metabolic hallmarks of P_i limitation in crop plants, we studied the metabolic response of barley leaves over the first 7 d of P_i stress, and the relationship of primary metabolites with leaf P_i levels and leaf biomass. The abundance of leaf P_i , Tyr and shikimate were significantly different between low Pi and control plants 1 h after transfer of the plants to low P_i . Combining these data with ¹⁵ N metabolic labelling, we show that over the first 48 h of P_i limitation, metabolic flux through the N assimilation and aromatic amino acid pathways is increased. We propose that together with a shift in amino acid metabolism in the chloroplast a transient restoration of the energetic and redox state of the leaf is achieved. Correlation analysis of metabolite abundances revealed a central role for major amino acids in P_i stress, appearing to modulate partitioning of soluble sugars between amino acid and carboxylate synthesis, thereby limiting leaf biomass accumulation when external P_i is low.

One way. Or another? Iron uptake in plants

Iron (Fe) and phosphorus (P), the latter taken up by plants as phosphate (Pi), are two essential nutrients that determine species distribution and often limit crop yield as a result of their low availability in most soils. Pi-deficient plants improve the interception of Pi by increasing the density of root hairs, thereby expanding the volume of soil to be explored. The increase in root-hair frequency results mainly from attenuated primary root growth, a process that was shown to be dependent on the availability of external Fe. Recent data support a hypothesis in which cell elongation during Pi starvation is tuned by depositing Fe in the apoplast of cortical cells in the root elongation zone. Uptake of Fe under Pi starvation appears to proceed via an alternative, as yet unidentified, route that bypasses the default Fe transporter. Fe deposits acquired through this noncanonical Fe-uptake pathway compromises cell-to-cell communication that is critical for proper morphogenesis of epidermal cells and leads to shorter cells and higher root-hair density. An auxiliary Fe-uptake system might not only be crucial for recalibrating cell elongation in Pi-deficient plants but may also have general importance for growth on Pi- or Fe-poor soils by balancing the Pi and Fe supply.

An Arabidopsis ABC Transporter Mediates Phosphate Deficiency-Induced Remodeling of Root Architecture by Modulating Iron Homeostasis in Roots

The remodeling of root architecture is a major developmental response of plants to phosphate (Pi) deficiency and is thought to enhance a plant's ability to forage for the available Pi in topsoil. The underlying mechanism controlling this response, however, is poorly understood. In this study, we identified an Arabidopsis mutant, hps10 (hypersensitive to Pi starvation 10), which is morphologically normal under Pi sufficient condition but shows increased inhibition of primary root growth and enhanced production of lateral roots under Pi deficiency. hps10 is a previously identified allele (als3-3) of the ALUMINUM SENSITIVE3 (ALS3) gene, which is involved in plant tolerance to aluminum toxicity. Our results show that ALS3 and its interacting protein AtSTAR1 form an ABC transporter complex in the tonoplast. This protein complex mediates a highly electrogenic transport in Xenopus oocytes. Under Pi deficiency, als3 accumulates higher levels of Fe³⁺ in its roots than the wild type does. In Arabidopsis, LPR1 (LOW PHOSPHATE ROOT1) and LPR2 encode ferroxidases, which when mutated, reduce Fe³⁺ accumulation in roots and cause root growth to be insensitive to Pi deficiency. Here, we provide compelling evidence showing that ALS3 cooperates with LPR1/2 to regulate Pi deficiency-induced remodeling of root architecture by modulating Fe homeostasis in roots.

StMYB44 negatively regulates phosphate transport by suppressing expression of PHOSPHATE1 in potato

Phosphorus is an important macronutrient for plant growth, but often deficient in soil. To understand the molecular basis of the complex responses of potato (Solanum tuberosum L.) to phosphate (Pi) deficiency stress, the RNA-Seq approach was taken to identify genes responding to Pi starvation in potato roots. A total of 359 differentially expressed genes were identified, among which the Solanum tuberosum transcription factor gene MYB44 (StMYB44) was found to be down-regulated by Pi starvation. StMYB44 was ubiquitously expressed in potato tissues and organs, and StMYB44 protein was exclusively localized in the nucleus. Overexpression of StMYB44 in potato resulted in lower accumulation of Pi in shoots. Transcriptomic analysis indicated that the abundance of S. tuberosum PHOSPHATE1 (StPHO1), a Pi transport-related gene, was reduced in StMYB44 overexpression lines. In contrast, knock-out of StMYB44 by a CRISPR/Cas9 system failed to increase transcription of StPHO1. Moreover, StMYB44 was found to interact in the nucleus with AtWRKY6, a known Arabidopsis transcription factor directly regulating PHO1 expression, and StWRKY6, indicating that StMYB44 could be a member of the regulatory complex controlling transcription of StPHO1. Taken together, our study demonstrates that StMYB44 negatively regulates Pi transport in potato by suppressing StPHO1 expression.

Adaptation of the symbiotic Mesorhizobium-chickpea relationship to phosphate deficiency relies on reprogramming of whole-plant metabolism

Low inorganic phosphate (Pi) availability is a major constraint for efficient nitrogen fixation in legumes, including chickpea. To elucidate the mechanisms involved in nodule acclimation to low Pi availability, two Mesorhizobium-chickpea associations exhibiting differential symbiotic performances, Mesorhizobium ciceri CP-31 (McCP-31)-chickpea and Mesorhizobium mediterranum SWRI9 (MmSWRI9)-chickpea, were comprehensively studied under both control and low Pi conditions. MmSWRI9-chickpea showed a lower symbiotic efficiency under low Pi availability than McCP-31-chickpea as evidenced by reduced growth parameters and down-regulation of nifD and nifK These differences can be attributed to decline in Pi level in MmSWRI9-induced nodules under low Pi stress, which coincided with up-regulation of several key Pi starvation-responsive genes, and accumulation of asparagine in nodules and the levels of identified amino acids in Pi-deficient leaves of MmSWRI9-inoculated plants exceeding the shoot nitrogen requirement during Pi starvation, indicative of nitrogen feedback inhibition. Conversely, Pi levels increased in nodules of Pi-stressed McCP-31-inoculated plants, because these plants evolved various metabolic and biochemical strategies to maintain nodular Pi homeostasis under Pi deficiency. These adaptations involve the activation of alternative pathways of carbon metabolism, enhanced production and exudation of organic acids from roots into the rhizosphere, and the ability to protect nodule metabolism against Pi deficiency-induced oxidative stress. Collectively, the adaptation of symbiotic efficiency under Pi deficiency resulted from highly coordinated processes with an extensive reprogramming of whole-plant metabolism. The findings of this study will enable us to design effective breeding and genetic engineering strategies to enhance symbiotic efficiency in legume crops.

Deciphering Phosphate Deficiency-Mediated Temporal Effects on Different Root Traits in Rice Grown in a Modified Hydroponic System

Phosphate (Pi), an essential macronutrient for growth and development of plant, is often limiting in soils. Plants have evolved an array of adaptive strategies including modulation of root system architecture (RSA) for optimal acquisition of Pi. In rice, a major staple food, RSA is complex and comprises embryonically developed primary and seminal roots and post-embryonically developed adventitious and lateral roots. Earlier studies have used variant hydroponic systems for documenting the effects of Pi deficiency largely on primary root growth. Here, we report the temporal effects of Pi deficiency in rice genotype MI48 on 15 ontogenetically distinct root traits by using easy-to-assemble and economically viable modified hydroponic system. Effects of Pi deprivation became evident after 4 days- and 7 days-treatments on two and eight different root traits, respectively. The effects of Pi deprivation for 7 days were also evident on different root traits of rice genotype Nagina 22 (N22). There were genotypic differences in the responses of primary root growth along with lateral roots on it and the number and length of seminal and adventitious roots. Notably though, there were attenuating effects of Pi deficiency on the lateral roots on seminal and adventitious roots and total root length in both these genotypes. The study thus revealed both differential and comparable effects of Pi deficiency on different root traits in these genotypes. Pi deficiency also triggered reduction in Pi content and induction of several Pi starvation-responsive (PSR) genes in roots of MI48. Together, the analyses validated the fidelity of this modified hydroponic system for documenting Pi deficiency-mediated effects not only on different traits of RSA but also on physiological and molecular responses.

An Inventory of Nutrient-Responsive Genes in Arabidopsis Root Hairs

Root hairs, single cell extensions of root epidermal cells that are critically involved in the acquisition of mineral nutrients, have proven to be an excellent model system for studying plant cell growth. More recently, omics-based systems biology approaches have extended the model function of root hairs toward functional genomic studies. While such studies are extremely useful to decipher the complex mechanisms underlying root hair morphogenesis, their importance for the performance and fitness of the plant puts root hairs in the spotlight of research aimed at elucidating aspects with more practical implications. Here, we mined transcriptomic and proteomic surveys to catalog genes that are preferentially expressed in root hairs and responsive to nutritional signals. We refer to this group of genes as the root hair trophomorphome. Our analysis shows that the activity of genes within the trophomorphome is regulated at both the transcriptional and post-transcriptional level with the mode of regulation being related to the function of the gene product. A core set of proteins functioning in cell wall modification and protein transport was defined as the backbone of the trophomorphome. In addition, our study shows that homeostasis of reactive oxygen species and redox regulation plays a key role in root hair trophomorphogenesis.

Exposure of barley plants to low Pi leads to rapid changes in root respiration that correlate with specific alterations in amino acid substrates

The majority of inorganic phosphate (Pi ) stress studies in plants have focused on the response after growth has been retarded. Evidence from transcript analysis, however, shows that a Pi -stress specific response is initiated within minutes of transfer to low Pi and in crop plants precedes the expression of Pi transporters and depletion of vacuolar Pi reserves by days. In order to investigate the physiological and metabolic events during early exposure to low Pi in grain crops, we monitored the response of whole barley plants during the first hours following Pi withdrawal. Lowering the concentration of Pi led to rapid changes in root respiration and leaf gas exchange throughout the early phase of the light course. Combining amino and organic acid analysis with (15) N labelling we show a root-specific effect on nitrogen metabolism linked to specific substrates of respiration as soon as 1 h following Pi withdrawal; this explains the respiratory responses observed and was confirmed by stimulation of respiration by exogenous addition of these respiratory substrates to roots. The rapid adjustment of substrates for respiration in roots during short-term Pi -stress is highlighted and this could help guide roots towards Pi -rich soil patches without compromising biomass accumulation of the plant.

Phosphatidylinositol phosphate 5-kinase genes respond to phosphate deficiency for root hair elongation in Arabidopsis thaliana

Plants drastically alter their root system architecture to adapt to different underground growth conditions. During phosphate (Pi) deficiency, most plants including Arabidopsis thaliana enhance the development of lateral roots and root hairs, resulting in bushy and hairy roots. To elucidate the signal pathway specific for the root hair elongation response to Pi deficiency, we investigated the expression of type-B phosphatidylinositol phosphate 5-kinase (PIP5K) genes, as a quantitative factor for root hair elongation in Arabidopsis. At young seedling stages, the PIP5K3 and PIP5K4 genes responded to Pi deficiency in steady-state transcript levels via PHR1-binding sequences (P1BSs) in their upstream regions. Both pip5k3 and pip5k4 single mutants, which exhibit short-root-hair phenotypes, remained responsive to Pi deficiency for root hair elongation; however the pip5k3pip5k4 double mutant exhibited shorter root hairs than the single mutants, and lost responsiveness to Pi deficiency at young seedling stages. In the tactical complementation line in which modified PIP5K3 and PIP5K4 genes with base substitutions in their P1BSs were co-introduced into the double mutant, root hairs of young seedlings had normal lengths under Pi-sufficient conditions, but were not responsive to Pi deficiency. From these results, we conclude that a Pi-deficiency signal is transferred to the pathway for root hair elongation via the PIP5K genes.