A novel glycerophosphodiester phosphodiesterase improves phosphate deficiency tolerance in rice

The Myb73-GDPD2-GA2ox1 transcriptional regulatory module confers phosphate deficiency tolerance in soybean

Phosphorus is indispensable in agricultural production. An increasing food supply requires more efficient use of phosphate due to limited phosphate resources. However, how crops regulate phosphate efficiency remains largely unknown. Here, we identified a major quantitative trait locus, qPE19, that controls 7 low-phosphate (LP)-related traits in soybean (Glycine max) through linkage mapping and genome-wide association studies. We identified the gene responsible for qPE19 as GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE2 (GmGDPD2), and haplotype 5 represents the optimal allele favoring LP tolerance. Overexpression of GmGDPD2 significantly affects hormone signaling and improves root architecture, phosphate efficiency and yield-related traits; conversely, CRISPR/Cas9-edited plants show decreases in these traits. GmMyb73 negatively regulates GmGDPD2 by directly binding to its promoter; thus, GmMyb73 negatively regulates LP tolerance. GmGDPD2 physically interacts with GA 2-oxidase 1 (GmGA2ox1) in the plasma membrane, and overexpressing GmGA2ox1 enhances LP-associated traits, similar to GmGDPD2 overexpression. Analysis of double mutants for GmGDPD2 and GmGA2ox1 demonstrated that GmGDPD2 regulates LP tolerance likely by influencing auxin and gibberellin dose-associated cell division in the root. These results reveal a regulatory module that plays a major role in regulating LP tolerance in soybeans and is expected to be utilized to develop phosphate-efficient varieties to enhance soybean production, particularly in phosphate-deficient soils.

An update on Glycerophosphodiester Phosphodiesterases; From Bacteria to Human

The hydrolysis of deacylated glycerophospholipids into sn-glycerol 3-phosphate and alcohol is facilitated by evolutionarily conserved proteins known as glycerophosphodiester phosphodiesterases (GDPDs). These proteins are crucial for the pathogenicity of bacteria and for bioremediation processes aimed at degrading organophosphorus esters that pose a hazard to both humans and the environment. Additionally, GDPDs are enzymes that respond to multiple nutrients and could potentially serve as candidate genes for addressing deficiencies in zinc, iron, potassium, and especially phosphate in important plants like rice. In mammals, glycerophosphodiesterases (GDEs) play a role in regulating osmolytes, facilitating the biosynthesis of anandamine, contributing to the development of skeletal muscle, promoting the differentiation of neurons and osteoblasts, and influencing pathological states. Due to their capacity to enhance a plant's ability to tolerate various nutrient deficiencies and their potential as pharmaceutical targets in humans, GDPDs have received increased attention in recent times. This review provides an overview of the functions of GDPD families as vital and resilient enzymes that regulate various pathways in bacteria, plants, and humans.

Transcriptional responses of the marine diatom Chaetoceros tenuissimus to phosphate deficiency

The planktonic diatom Chaetoceros tenuissimus sometimes forms blooms in coastal surface waters where dissolved inorganic phosphorus (P) is typically deficient. To understand the molecular mechanisms for survival under P-deficient conditions, we compared whole transcripts and metabolites with P-sufficient conditions using stationary growth cells. Under P-deficient conditions, cell numbers and photosynthetic activities decreased as cells entered the stationary growth phase, with downregulation of transcripts related to the Calvin cycle and glycolysis/gluconeogenesis. Therefore, metabolites varied across nutritional conditions. Alkaline phosphatase, phosphodiesterase, phytase, phosphate transporter, and transcription factor genes were drastically upregulated under dissolved inorganic P deficiency. Genes related to phospholipid degradation and nonphospholipid synthesis were also upregulated. These results indicate that C. tenuissimus rearranges its membrane composition from phospholipids to nonphospholipids to conserve phosphate. To endure in P-deficient conditions, C. tenuissimus modifies its gene responses, suggesting a potential survival strategy in nature.

Comparative biochemical and transcriptomic analysis reveals the phosphate-starving tolerance of two ramie varieties

Ramie (Boehmeria nivea L.) is a highly valued fiber crop. Its yield is often limited by lack of available phosphate (Pi) in the soil, but the underlying molecular mechanisms of ramie's response to Pi deficiency remain largely unknown. To investigate how ramie adapts to low Pi stress, we selected a low Pi-tolerant variety (H-5) and a low Pi-sensitive variety (XYL), and conducted a biochemical and transcriptomic analysis on roots and leaves of both varieties. After subjecting the plants to Pi-deficient and Pi-sufficient conditions for 15 days, we found that H-5 exhibited higher dry weight, longer root systems, and higher levels of Pi, galactolipids, and organic acids when subjected to Pi deprivation, compared to XYL. Transcriptomic analysis further revealed that Pi-responsive genes involved in lipid metabolism, Pi transport, organic acid synthesis, and acid phosphatase activities were more induced in the tolerant variety H-5. Furthermore, weighted gene co-expression network analysis (WGCNA) identified five hub genes, including phosphate transporter, SPX domain-containing protein and sulfoquinovosyl transferase, which played key roles in low Pi tolerance in ramie. The present study will broaden our comprehension of the differences and molecular mechanisms of different ramie cultivars in response to Pi starvation, and lay a foundation for future agronomic improvements in ramie and other fiber crops.

Integration of proteome and metabolome profiling to reveal heat stress response and tolerance mechanisms of Serratia sp. AXJ-M for the bioremediation of papermaking black liquor

The use of thermophilic bacteria for treating paper black liquor seems to be an efficient bioremediation strategy. In our previous work, the lignin-degrading bacterium Serratia sp. AXJ-M exhibited excellent heat tolerance ability. However, the molecular mechanism of its response to heat stress is unknown. Therefore, the heat stress response of AXJ-M was investigated using morphological and analytical methods. A comparative genomics analysis revealed interesting insights into the adaptability of the genetic basis of AXJ-M to harsh environments. Moreover, TMT quantitative proteomic analysis and parallel reaction monitoring (PRM) assays revealed that proteins related to both component systems, ABC transporters, carbohydrate, and amino metabolism, energy metabolism, etc., were differentially expressed. The non-targeted metabolome analysis revealed that the metabolic pathways associated with the fatty acid and amino acid biosynthesis and metabolism, together with the TCA cycle were most significantly enriched. Furthermore, integrated omics suggested that AXJ-M made metabolic adaptations to compensate for the increased energy demand caused by adverse environmental stimuli. The dominant heat regulator HspQ mediated heat adaptation of AXJ-M at high temperatures and modulated DyP expression. To summarize, the present study sheds light on the effect of high temperature on the lignin-degrading bacterium and its tolerance and underlying regulatory mechanisms.

Metabolic footprints in phosphate-starved plants

Plants' requirement of Phosphorus (P) as an essential macronutrient is obligatory for their normal growth and metabolism. Besides restricting plants' primary growth, P depletion affects both primary and secondary metabolism and leads to altered levels of sugars, metabolites, amino acids, and other secondary compounds. Such metabolic shifts help plants optimize their metabolism and growth under P limited conditions. Under P deprivation, both sugar levels and their mobilization change that influences the expression of Pi starvation-inducible genes. Increased sugar repartitioning from shoot to root help root growth and organic acids secretion that in turn promotes phosphate (Pi) uptake from the soil. Other metabolic changes such as lipid remodeling or P reallocation from older to younger leaves release the P from its bound forms in the cell. In this review, we summarize the metabolic footprinting of Pi-starved plants with respect to the benefits offered by such metabolic changes to intracellular Pi homeostasis.

Role of glycerophosphodiester phosphodiesterase in rice leaf blades in elevated CO2 environments

Glycerophosphodiester phosphodiesterase (GDPD; EC 3.1.4.46) is involved in plant phosphate (Pi) utilization and its expression is upregulated under phosphorus (P)-deficient conditions. Although rice was grown under P-sufficient conditions, the transcript levels of specific OsGDPD were upregulated in mature rice leaf blades (LB) in elevated CO₂ (eCO₂ ) environments. Expression and subcellular localization of GDPD, and contents of Pi, sugar phosphates and carbohydrates were analysed to clarify the physiological function of GDPD in rice under eCO₂ . Under eCO₂ , expression of specific OsGDPD increased only in mature rice LB in which low Pi concentrations were observed. Moreover, eCO₂ -induced OsGDPD2 and OsGDPD3 were localized in the plastid, indicating that GDPD2 and GDPD3 may be related to plastidic functions, such as carbon assimilation. Although rice LB contained more carbohydrates under eCO₂ than under ambient CO₂ , the phosphoglucose content decreased under eCO₂ , suggesting that the need for excess phosphoglucose to synthesize carbohydrates under eCO₂ causes a local Pi deficiency. Furthermore, we confirmed that glycerol-3-phosphate produced by the catalysis of GDPD from glycerophosphodiester contributes to carbohydrate accumulation in rice LB. Our findings suggest that local Pi deficiency due to excess carbohydrate accumulation under eCO₂ influences GDPD to enhance glycerophosphodiester hydrolysis.

Adaptive strategies of plants to conserve internal phosphorus under P deficient condition to improve P utilization efficiency

Phosphorus (P) is one of the limiting factors for plant growth and productivity due to its slow diffusion and immobilization in the soil which necessitates application of phosphatic fertilizers to meet the crop demand and obtain maximum yields. However, plants have evolved mechanisms to adapt to low P stress conditions either by increasing acquisition (alteration of belowground processes) or by internal inorganic P (Pi) utilization (cellular Pi homeostasis) or both. In this review, we have discussed the adaptive strategies that conserve the use of P and maintain cellular Pi homeostasis in the cytoplasm. These strategies involve modification in membrane lipid composition, flavanol/anthocyanin level, scavenging and reutilization of Pi adsorbed in cell wall pectin, remobilization of Pi during senescence by enzymes like RNases and purple acid phosphatases, alternative mitochondrial electron transport, and glycolytic pathways. The remobilization of Pi from senescing tissues and its internal redistribution to various cellular organelles is mediated by various Pi transporters. Although much efforts have been made to enhance P acquisition efficiency, an understanding of the physiological mechanisms conserving internal Pi and their manipulation would be useful for plants that can utilize P more efficiently to produce optimum growth per unit P uptake.

Characterization of the PHOSPHATE RESPONSE 2-dependent and -independent Pi-starvation response secretome in rice

Many proteins secreted from plant cells into the surrounding extracellular space help maintain cell structure and regulate stress responses in the external environment. In this study, under Pi-replete and depleted conditions, 652 high-confidence secreted proteins were quantified from wild-type (WT) and PHOSPHATE RESPONSE 2 (OsPHR2)-overexpressing suspension-cultured cells (SCCs). These proteins were functionally grouped as phosphatases, signal transduction proteins, pathogen-related (PR) proteins, cell wall-remodeling proteins, and reactive oxygen species (ROS) metabolism proteins. Although PHOSPHATE RESPONSE (PHR) transcription factors regulate two-thirds of Pi-responsive genes at the transcriptional level, only 30.6% of the Pi-starvation-regulated secreted proteins showed significant changes in OsPHR2-overexpressing SCCs. The OsPHR2-dependent systemic Pi signaling pathway mainly regulates phosphatases and PR proteins, which are involved in the utilization of organophosphate, pathogen resistance, and colonization by rhizosphere microorganisms. The OsPHR2-independent local Pi signaling pathway, on the other hand, largely regulated ROS metabolism proteins, cell wall-remodeling proteins, and signal transduction proteins, which are involved in modifying cell wall structure and root architecture. The functions of differentially expressed secreted proteins between WT and OsPHR2-overexpressing plants under Pi-sufficient and Pi-deficient conditions were further confirmed by analysis of the acid phosphatase activity, ROS content, and cell wall composition.

Advances in Plant Lipid Metabolism Responses to Phosphate Scarcity

Low phosphate (Pi) availability in soils severely limits crop growth and production. Plants have evolved to have numerous physiological and molecular adaptive mechanisms to cope with Pi starvation. The release of Pi from membrane phospholipids is considered to improve plant phosphorus (P) utilization efficiency in response to Pi starvation and accompanies membrane lipid remodeling. In this review, we summarize recent discoveries related to this topic and the molecular basis of membrane phospholipid alteration and triacylglycerol metabolism in response to Pi depletion in plants at different subcellular levels. These findings will help to further elucidate the molecular mechanisms underlying plant adaptation to Pi starvation and thus help to develop crop cultivars with high P utilization efficiency.

Monogalactosyl diacylglycerol synthase 3 affects phosphate utilization and acquisition in rice

Galactolipids are essential to compensate for the loss of phospholipids by 'membrane lipid remodelling' in plants under phosphorus (P) deficiency conditions. Monogalactosyl diacylglycerol (MGDG) synthases catalyse the synthesis of MGDG which is further converted into digalactosyl diacylglycerol (DGDG), later replacing phospholipids in the extraplastidial membranes. However, the roles of these enzymes are not well explored in rice. In this study, the rice MGDG synthase 3 gene (OsMGD3) was identified and functionally characterized. We showed that the plant phosphate (Pi) status and the transcription factor PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) are involved in the transcriptional regulation of OsMGD3. CRISPR/Cas9 knockout and overexpression lines of OsMGD3 were generated to explore its potential role in rice adaptation to Pi deficiency. Compared with the wild type, OsMGD3 knockout lines displayed a reduced Pi acquisition and utilization while overexpression lines showed an enhancement of the same. Further, OsMGD3 showed a predominant role in roots, altering lateral root growth. Our comprehensive lipidomic analysis revealed a role of OsMGD3 in membrane lipid remodelling, in addition to a role in regulating diacylglycerol and phosphatidic acid contents that affected the expression of Pi transporters. Our study highlights the role of OsMGD3 in affecting both internal P utilization and P acquisition in rice.

Transcriptome and hyperspectral profiling allows assessment of phosphorus nutrient status in rice under field conditions

Phosphorus (P) is one of the macronutrients indispensable for crop production, and therefore it is important to understand the potential of plants to adapt to low P conditions. We compared growth and leaf genome-wide transcriptome of four rice cultivars during growth between two fields with different amount of available phosphate and further analysed the acceptable range of P levels for normal growth from the view of both appearance traits and internal P nutrient status, which was measured by profiling the expression of the P indicator gene. This demonstrated that rice plants have a robustness to moderate P-deficient conditions expressing a system for P acquisition and usage without any effects on yield potential and that P indicator gene expression could be a useful index for early diagnosis of P status in plants. To develop a simple method for assessment of P status, we tried to predict the expression level using reflectance spectroscopy and hyperspectral imaging, thereby providing models with good performance. Our findings suggest that rice plants have the potential to adapt to moderate low P conditions in the field and showed that the hyperspectral technique is one of the useful tools for simple measurement of molecular-level dynamics reflecting internal nutrient conditions.

OsJAZ11 regulates spikelet and seed development in rice

Seed size is one of the major determinants of seed weight and eventually, crop yield. As the global population is increasing beyond the capacity of current food production, enhancing seed size is a key target for crop breeders. Despite the identification of several genes and QTLs, current understanding about the molecular regulation of seed size/weight remains fragmentary. In the present study, we report novel role of a jasmonic acid (JA) signaling repressor, OsJAZ11 controlling rice seed width and weight. Transgenic rice lines overexpressing OsJAZ11 exhibited up to a 14% increase in seed width and ~30% increase in seed weight compared to wild type (WT). Constitutive expression of OsJAZ11 dramatically influenced spikelet morphogenesis leading to extra glume-like structures, open hull, and abnormal numbers of floral organs. Furthermore, overexpression lines accumulated higher JA levels in spikelets and developing seeds. Expression studies uncovered altered expression of JA biosynthesis/signaling and MADS box genes in overexpression lines compared to WT. Yeast two-hybrid and pull-down assays revealed that OsJAZ11 interacts with OsMADS29 and OsMADS68. Remarkably, expression of OsGW7, a key negative regulator of grain size, was significantly reduced in overexpression lines. We propose that OsJAZ11 participates in the regulation of seed size and spikelet development by coordinating the expression of JA-related, OsGW7 and MADS genes.

Mechanisms Underlying Soybean Response to Phosphorus Deficiency through Integration of Omics Analysis

Low phosphorus (P) availability limits soybean growth and yield. A set of potential strategies for plant responses to P deficiency have been elucidated in the past decades, especially in model plants such as Arabidopsis thaliana and rice (Oryza sativa). Recently, substantial efforts focus on the mechanisms underlying P deficiency improvement in legume crops, especially in soybeans (Glycine max). This review summarizes recent advances in the morphological, metabolic, and molecular responses of soybean to phosphate (Pi) starvation through the combined analysis of transcriptomics, proteomics, and metabolomics. Furthermore, we highlight the functions of the key factors controlling root growth and P homeostasis, base on which, a P signaling network in soybean was subsequently presumed. This review also discusses current barriers and depicts perspectives in engineering soybean cultivars with high P efficiency.

Mechanisms for improving phosphorus utilization efficiency in plants

BACKGROUND

Limitation of plant productivity by phosphorus (P) supply is widespread and will probably increase in the future. Relatively large amounts of P fertilizer are applied to sustain crop growth and development and to achieve high yields. However, with increasing P application, plant P efficiency generally declines, which results in greater losses of P to the environment with detrimental consequences for ecosystems.

SCOPE

A strategy for reducing P input and environmental losses while maintaining or increasing plant performance is the development of crops that take up P effectively from the soil (P acquisition efficiency) or promote productivity per unit of P taken up (P utilization efficiency). In this review, we describe current research on P metabolism and transport and its relevance for improving P utilization efficiency.

CONCLUSIONS

Enhanced P utilization efficiency can be achieved by optimal partitioning of cellular P and distributing P effectively between tissues, allowing maximum growth and biomass of harvestable plant parts. Knowledge of the mechanisms involved could help design and breed crops with greater P utilization efficiency.

PHOSPHATE STARVATION RESPONSE transcription factors enable arbuscular mycorrhiza symbiosis

Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants and Glomeromycotina fungi. AM is important for ecosystem health and functioning as the fungi critically support plant performance by providing essential mineral nutrients, particularly the poorly accessible phosphate, in exchange for organic carbon. AM fungi colonize the inside of roots and this is promoted at low but inhibited at high plant phosphate status, while the mechanistic basis for this phosphate-dependence remained obscure. Here we demonstrate that a major transcriptional regulator of phosphate starvation responses in rice PHOSPHATE STARVATION RESPONSE 2 (PHR2) regulates AM. Root colonization of phr2 mutants is drastically reduced, and PHR2 is required for root colonization, mycorrhizal phosphate uptake, and yield increase in field soil. PHR2 promotes AM by targeting genes required for pre-contact signaling, root colonization, and AM function. Thus, this important symbiosis is directly wired to the PHR2-controlled plant phosphate starvation response.

PHOSPHATE STARVATION RESPONSE transcription factors enable arbuscular mycorrhiza symbiosis

Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants and Glomeromycotina fungi. AM is important for ecosystem health and functioning as the fungi critically support plant performance by providing essential mineral nutrients, particularly the poorly accessible phosphate, in exchange for organic carbon. AM fungi colonize the inside of roots and this is promoted at low but inhibited at high plant phosphate status, while the mechanistic basis for this phosphate-dependence remained obscure. Here we demonstrate that a major transcriptional regulator of phosphate starvation responses in rice PHOSPHATE STARVATION RESPONSE 2 (PHR2) regulates AM. Root colonization of phr2 mutants is drastically reduced, and PHR2 is required for root colonization, mycorrhizal phosphate uptake, and yield increase in field soil. PHR2 promotes AM by targeting genes required for pre-contact signaling, root colonization, and AM function. Thus, this important symbiosis is directly wired to the PHR2-controlled plant phosphate starvation response.

Metabolomics combined with physiology and transcriptomics reveals how Citrus grandis leaves cope with copper-toxicity

Limited data are available on metabolic responses of plants to copper (Cu)-toxicity. Firstly, we investigated Cu-toxic effects on metabolomics, the levels of free amino acids, NH₄⁺-N, NO₃^--N, total nitrogen, total soluble proteins, total phenolics, lignin, reduced glutathione (GSH) and malondialdehyde, and the activities of nitrogen-assimilatory enzymes in 'Shatian' pummelo (Citrus grandis) leaves. Then, a conjoint analysis of metabolomics, physiology and transcriptomics was performed. Herein, 59 upregulated [30 primary metabolites (PMs) and 29 secondary metabolites (SMs)] and 52 downregulated (31 PMs and 21 SMs) metabolites were identified in Cu-toxic leaves. The toxicity of Cu to leaves was related to the Cu-induced accumulation of NH₄⁺ and decrease of nitrogen assimilation. Metabolomics combined with physiology and transcriptomics revealed some adaptive responses of C. grandis leaves to Cu-toxicity, including (a) enhancing tryptophan metabolism and the levels of some amino acids and derivatives (tryptophan, phenylalanine, 5-hydroxy-l-tryptophan, 5-oxoproline and GSH); (b) increasing the accumulation of carbohydrates and alcohols and upregulating tricarboxylic acid cycle and the levels of some organic acids and derivatives (chlorogenic acid, quinic acid, d-tartaric acid and gallic acid o-hexoside); (c) reducing phospholipid (lysophosphatidylcholine and lysophosphatidylethanolamine) levels, increasing non-phosphate containing lipid [monoacylglycerol ester (acyl 18:2) isomer 1] levels, and inducing low-phosphate-responsive gene expression; and (d) triggering the biosynthesis of some chelators (total phenolics, lignin, l-trytamine, indole, eriodictyol C-hexoside, quercetin 5-O-malonylhexosyl-hexoside, N-caffeoyl agmatine, N'-p-coumaroyl agmatine, hydroxy-methoxycinnamate and protocatechuic acid o-glucoside) and vitamins and derivatives (nicotinic acid-hexoside, B₁ and methyl nicotinate). Cu-induced upregulation of many antioxidants could not protect Cu-toxic leaves from oxidative damage. To conclude, our findings corroborated the hypothesis that extensive reprogramming of metabolites was carried out in Cu-toxic C. grandis leaves in order to cope with Cu-toxicity.

Plant phospholipase D: novel structure, regulatory mechanism, and multifaceted functions with biotechnological application

Phospholipases D (PLDs) are important membrane lipid-modifying enzymes in eukaryotes. Phosphatidic acid, the product of PLD activity, is a vital signaling molecule. PLD-mediated lipid signaling has been the subject of extensive research leading to discovery of its crystal structure. PLDs are involved in the pathophysiology of several human diseases, therefore, viewed as promising targets for drug design. The availability of a eukaryotic PLD crystal structure will encourage PLD targeted drug designing. PLDs have been implicated in plants response to biotic and abiotic stresses. However, the molecular mechanism of response is not clear. Recently, several novel findings have shown that PLD mediated modulation of structural and developmental processes, such as: stomata movement, root growth and microtubule organization are crucial for plants adaptation to environmental stresses. Involvement of PLDs in regulating membrane remodeling, auxin mediated alteration of root system architecture and nutrient uptake to combat nitrogen and phosphorus deficiencies and magnesium toxicity is established. PLDs via vesicle trafficking modulate cytoskeleton and exocytosis to regulate self-incompatibility (SI) signaling in flowering plants, thereby contributes to plants hybrid vigor and diversity. In addition, the important role of PLDs has been recognized in biotechnologically important functions, including oil/TAG synthesis and maintenance of seed quality. In this review, we describe the crystal structure of a plant PLD and discuss the molecular mechanism of catalysis and activity regulation. Further, the role of PLDs in regulating plant development under biotic and abiotic stresses, nitrogen and phosphorus deficiency, magnesium ion toxicity, SI signaling and pollen tube growth and in important biotechnological applications has been discussed.

OsJAZ11 regulates phosphate starvation responses in rice

OsJAZ11 regulates phosphate homeostasis by suppressing jasmonic acid signaling and biosynthesis in rice roots. Jasmonic Acid (JA) is a key plant signaling molecule which negatively regulates growth processes including root elongation. JAZ (JASMONATE ZIM-DOMAIN) proteins function as transcriptional repressors of JA signaling. Therefore, targeting JA signaling by deploying JAZ repressors may enhance root length in crops. In this study, we overexpressed JAZ repressor OsJAZ11 in rice to alleviate the root growth inhibitory action of JA. OsJAZ11 is a low phosphate (Pi) responsive gene which is transcriptionally regulated by OsPHR2. We report that OsJAZ11 overexpression promoted primary and seminal root elongation which enhanced Pi foraging. Expression studies revealed that overexpression of OsJAZ11 also reduced Pi starvation response (PSR) under Pi limiting conditions. Moreover, OsJAZ11 overexpression also suppressed JA signaling and biosynthesis as compared to wild type (WT). We further demonstrated that the C-terminal region of OsJAZ11 was crucial for stimulating root elongation in overexpression lines. Rice transgenics overexpressing truncated OsJAZ11ΔC transgene (i.e., missing C-terminal region) exhibited reduced root length and Pi uptake. Interestingly, OsJAZ11 also regulates Pi homeostasis via physical interaction with a key Pi sensing protein, OsSPX1. Our study highlights the functional connections between JA and Pi signaling and reveals JAZ repressors as a promising candidate for improving low Pi tolerance of elite rice genotypes.

OsUEV1B, an Ubc enzyme variant protein, is required for phosphate homeostasis in rice

Phosphorus is a crucial macronutrient for plant growth and development. The mechanisms for maintaining inorganic phosphate (Pi) homeostasis in rice are not well understood. The ubiquitin-conjugating enzyme variant protein OsUEV1B was previously found to interact with OsUbc13 and mediate lysine63-linked polyubiquitination. In the present study, we found OsUEV1B was specifically inhibited by Pi deficiency, and was localized in the nucleus and cytoplasm. Both osuev1b mutant and OsUEV1B-RNA interference (RNAi) lines displayed serious symptoms of toxicity due to Pi overaccumulation. Some Pi starvation inducible and phosphate transporter genes were upregulated in osuev1b mutant and OsUEV1B-RNAi plants in association with enhanced Pi acquisition, and representative Pi starvation responses, including stimulation of acid phosphatase activity and root hair growth, were also activated in the presence of sufficient Pi. A yeast two-hybrid screen revealed an interaction between OsUEV1B and OsVDAC1, which was confirmed by bimolecular fluorescence complementation and firefly split-luciferase complementation assays. OsVDAC1 encoded a voltage-dependent anion channel protein localized in the mitochondria, and OsUbc13 was shown to interact with OsVDAC1 via yeast two-hybrid and bimolecular fluorescence complementation assays. Under sufficient Pi conditions, similar to osuev1b, a mutation in OsVDAC1 resulted in significantly greater Pi concentrations in the roots and second leaves, improved acid phosphatase activity, and enhanced expression of the Pi starvation inducible and phosphate transporter genes compared with wild-type DongJin, whereas overexpression of OsVDAC1 had the opposite effects. OsUEV1B or OsVDAC1 knockout reduced the mitochondrial membrane potential and adenosine triphosphate levels. Moreover, overexpression of OsVDAC1 in osuev1b partially restored its high Pi concentration to a level between those of osuev1b and DongJin. Our results indicate that OsUEV1B is required for rice phosphate homeostasis.

The Dynamic Responses of Oil Palm Leaf and Root Metabolome to Phosphorus Deficiency

Inorganic phosphate (Pi) starvation is an important abiotic constraint that affects plant cellular homeostasis, especially in tropical regions with high acidic soil and less solubilizable Pi. In the current work, oil palm seedlings were hydroponically maintained under optimal Pi-supply and no Pi-supply conditions for 14 days, and metabolites were measured by gas chromatography-mass spectrometry (GC-MS), from leaves and roots, after seven and 14 days of treatment, to investigate biochemical pathways in relation to P-utilizing strategy. After seven days of limited Pi, plant leaves showed increased levels of most soluble sugars, and after 14 days, the sugars' level decrease, except for erythritol, mannose, fructose, and glucose, which showed the highest levels. Rather in root samples, there were different but overlapping alterations, mainly on sugars, amino acids, and organic acids. The leaf sample was shown to have the highest response of sugars with myo-inositol playing a vital role in the redistribution of sugars, while maltose levels increased, indicating active degradation of starch in the root. High levels of glycerol and stearate in both roots and leaves suggest the metabolism of storage lipids for cellular energy during Pi-deficient conditions.

Discovery of new genetic determinants of morphological plasticity in rice roots and shoots under phosphate starvation using GWAS

Phosphorus is an essential nutrient for plants that is often in short supply. In rice (Oryza sativa L.), inorganic phosphate (P_i) deficiency leads to various physiological disorders that consequently affect plant productivity. In this study, a large-scale phenotyping experiment using 160 Vietnamese rice landraces was performed under greenhouse conditions, by employing an alpha lattice design with three replicates, to identify quantitative trait loci (QTLs) associated with plant growth inhibition caused by P_i deficiency. Rice plantlets were grown for six weeks in the PVC sand column (16 cm diameter × 80 cm height) supplied with P_i-deficient medium (10 μM P) or full-P_i Yoshida medium (320 μM P). The effects of P_i deficiency on the number of crown roots, root length, shoot length, root weight, shoot weight and total weight were studied. From 36 significant markers identified using a genome-wide association study, 21 QTLs associated with plant growth inhibition under P_i starvation were defined. In total, 158 candidate genes co-located with the defined QTLs were identified. Interestingly, one QTL (qRST9.14) was associated with all three weight-traits. The co-located gene GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE 13 was found to be potentially involved in P_i transport. Understanding the molecular mechanisms of Pi-starvation responses, and identifying the potential QTLs responsible for low-P_i stress tolerance, will provide valuable information for developing new varieties tolerant of low-P_i conditions.

Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean

Throughout the growing season, crops experience a multitude of short periods of various abiotic stresses. These stress events have long-term impacts on plant performance and yield. It is imperative to improve our understanding of the genes and biological processes underlying plant stress tolerance to mitigate end of season yield loss. The majority of studies examining transcriptional changes induced by stress focus on single stress events. Few studies have been performed in model or crop species to examine transcriptional responses of plants exposed to repeated or sequential stress exposure, which better reflect field conditions. In this study, we examine the transcriptional profile of soybean plants exposed to iron deficiency stress followed by phosphate deficiency stress (-Fe-Pi). Comparing this response to previous studies, we identified a core suite of genes conserved across all repeated stress exposures (-Fe-Pi, -Fe-Fe, -Pi-Pi). Additionally, we determined transcriptional response to sequential stress exposure (-Fe-Pi) involves genes usually associated with reproduction, not stress responses. These findings highlight the plasticity of the plant transcriptome and the complexity of unraveling stress response pathways.

Quantitative Proteomics Reveals that GmENO2 Proteins Are Involved in Response to Phosphate Starvation in the Leaves of Glycine max L

Soybean (Glycine max L.) is a major crop providing important source for protein and oil for human life. Low phosphate (LP) availability is a critical limiting factor affecting soybean production. Soybean plants develop a series of strategies to adapt to phosphate (Pi) limitation condition. However, the underlying molecular mechanisms responsible for LP stress response remain largely unknown. Here, we performed a label-free quantification (LFQ) analysis of soybean leaves grown under low and high phosphate conditions. We identified 267 induced and 440 reduced differential proteins from phosphate-starved leaves. Almost a quarter of the LP decreased proteins are involved in translation processes, while the LP increased proteins are accumulated in chlorophyll biosynthetic and carbon metabolic processes. Among these induced proteins, an enolase protein, GmENO2a was found to be mostly induced protein. On the transcriptional level, GmENO2a and GmENO2b, but not GmENO2c or GmENO2d, were dramatically induced by phosphate starvation. Among 14 enolase genes, only GmENO2a and GmENO2b genes contain the P1BS motif in their promoter regions. Furthermore, GmENO2b was specifically induced in the GmPHR31 overexpressing soybean plants. Our findings provide molecular insights into how soybean plants tune basic carbon metabolic pathway to adapt to Pi deprivation through the ENO2 enzymes.

Plant roots sense soil compaction through restricted ethylene diffusion

Soil compaction represents a major challenge for modern agriculture. Compaction is intuitively thought to reduce root growth by limiting the ability of roots to penetrate harder soils. We report that root growth in compacted soil is instead actively suppressed by the volatile hormone ethylene. We found that mutant Arabidopsis and rice roots that were insensitive to ethylene penetrated compacted soil more effectively than did wild-type roots. Our results indicate that soil compaction lowers gas diffusion through a reduction in air-filled pores, thereby causing ethylene to accumulate in root tissues and trigger hormone responses that restrict growth. We propose that ethylene acts as an early warning signal for roots to avoid compacted soils, which would be relevant to research into the breeding of crops resilient to soil compaction.

Physiological and Proteomic Analysis of Different Molecular Mechanisms of Sugar Beet Response to Acidic and Alkaline pH Environment

Soil pH is a major constraint to crop plant growth and production. Limited data are available on sugar beet growth status under different pH conditions. In this study, we analyzed the growth status and phenotype of sugar beet under pH 5, pH 7.5, and pH 9.5. It was found that the growth of sugar beet was best at pH 9.5 and worst at pH 5. The activities of superoxide dismutase (SOD) and peroxidase (POD) in leaves and roots increased as pH decreased from 9.5 to 5. Moreover, compared with pH 9.5, the levels of soluble sugar and proline in leaves increased significantly at pH 5. To explore the mechanisms of sugar beet response to different soil pH environments, we hypothesized that proteins play an important role in plant response to acidic and alkaline pH environment. Thus, the proteome changes in sugar beet modulated by pH treatment were accessed by TMT-based quantitative proteomic analysis. A total of three groups of differentially expressed proteins (DEPs) (pH 5 vs. pH 7.5, pH 9.5 vs. pH7.5 and pH 5 vs. pH 9.5) were identified in the leaves and roots of sugar beet. Several key proteins related to the difference of sugar beet response to acid (pH 5) and alkaline (pH 9.5) and involved in response to acid stress were detected and discussed. Moreover, based on proteomics results, QRT-PCR analysis confirmed that expression levels of three N transporters (NTR1, NRT2.1, and NRT2.5) in roots were relatively high under alkaline conditions (pH 9.5) compared with pH 5 or pH 7.5. The total nitrogen content of pH 9.5 in sugar beet was significantly higher than that of pH 7.5 and pH 5. These studies increase our understanding of the molecular mechanism of sugar beet response to different pH environments.

A genome-wide association study reveals the quantitative trait locus and candidate genes that regulate phosphate efficiency in a Vietnamese rice collection

The crucial role of phosphate (Pi) for plant alongside the expected depletion of non-renewable phosphate rock have created an urgent need for phosphate-efficient rice varieties. In this study, 157 greenhouse-grown Vietnamese rice landraces were treated under Pi-deficient conditions to discover the genotypic variation among biochemical traits, including relative efficiency of phosphorus use (REP), relative root to shoot weight ratio (RRSR), relative physiological phosphate use efficiency (RPPUE), and relative phosphate uptake efficiency (RPUpE). Plants were grown in Yoshida nutrient media with either a full (320 μM) or a low Pi supply (10 μM) over six weeks. This genome-wide association study led to the discovery of 31 significant single nucleotide polymorphisms, 18 quantitative trait loci (QTLs), and 85 candidate genes. A common QTL named qRPUUE9.16 was found among the three investigated traits. Some interesting candidate genes, such as PLASMA MEMBRANE PROTEIN1 (OsPM1), CALMODULIN-RELATED CALCIUM SENSOR PROTEIN 15 (OsCML15), phosphatases 2C (PP2C), STRESS-ACTIVATED PROTEIN KINASE (OsSAPK2), and GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASES (GDPD13), were found strongly correlated to the Pi starvation. RNA sequencing transcriptomes revealed that 45 out of 85 candidate genes were significantly regulated under Pi starvation. Furthermore, nearly two-thirds of genotypes did not possess the OsPsTOL1 gene; however, no significant difference was observed in response to Pi deficiency between genotypes with or without this gene, suggesting that other QTLs in rice may resist Pi starvation. These results provide new information on the genetics of nutrient use efficiency in rice and may potentially assist with developing more phosphate-efficient rice plants.

Comparative spatial lipidomics analysis reveals cellular lipid remodelling in different developmental zones of barley roots in response to salinity

Salinity-induced metabolic, ionic, and transcript modifications in plants have routinely been studied using whole plant tissues, which do not provide information on spatial tissue responses. The aim of this study was to assess the changes in the lipid profiles in a spatial manner and to quantify the changes in the elemental composition in roots of seedlings of four barley cultivars before and after a short-term salt stress. We used a combination of liquid chromatography-tandem mass spectrometry, inductively coupled plasma mass spectrometry, matrix-assisted laser desorption/ionization mass spectrometry imaging, and reverse transcription - quantitative real time polymerase chain reaction platforms to examine the molecular signatures of lipids, ions, and transcripts in three anatomically different seminal root tissues before and after salt stress. We found significant changes to the levels of major lipid classes including a decrease in the levels of lysoglycerophospholipids, ceramides, and hexosylceramides and an increase in the levels of glycerophospholipids, hydroxylated ceramides, and hexosylceramides. Our results revealed that modifications to lipid and transcript profiles in plant roots in response to a short-term salt stress may involve recycling of major lipid species, such as phosphatidylcholine, via resynthesis from glycerophosphocholine.

Mutational Analysis of OsPLDα1 Reveals Its Involvement in Phytic Acid Biosynthesis in Rice Grains

Phospholipids and phytic acid are important phosphorus (P)-containing compounds in rice grains. Phytic acid is considered as a major antinutrient, because the negatively charged phytic acid chelates cations, including essential micronutrients, and decreases their bioavailability to human beings and monogastric animals. To gain an insight into the interplay of these two kinds of phosphorus-containing metabolites, we used the CRISPR/Cas9 system to generate mutants of a phospholipase D gene (OsPLDα1) and analyzed the mutational effect on metabolites, including phytic acid in rice grains. Metabolic profiling of two ospldα1 mutants revealed depletion in the phosphatidic acid production and lower accumulation of cytidine diphosphate diacylglycerol and phosphatidylinositol. The mutants also showed significantly reduced phytic acid content as compared to their wild-type parent, and the expression of the key genes involved in the phytic acid biosynthesis was altered in the mutants. These results demonstrate that OsPLDα1 not only plays an important role in phospholipid metabolism but also is involved in phytic acid biosynthesis, most probably through the lipid-dependent pathway, and thus revealed a potential new route to regulate phytic acid biosynthesis in rice.

Integration of metabolome and transcriptome analyses highlights soybean roots responding to phosphorus deficiency by modulating phosphorylated metabolite processes

Phosphorus (P) is a major constituent of biomolecules in plant cells, and is an essential plant macronutrient. Low phosphate (Pi) availability in soils is a major constraint on plant growth. Although a complex variety of plant responses to Pi starvation has been well documented, few studies have integrated both global transcriptome and metabolome analyses to shed light on molecular mechanisms underlying metabolic responses to P deficiency. This study is the first time to investigate global profiles of metabolites and transcripts in soybean (Glycine max) roots subjected to Pi starvation through targeted liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS/MS) and RNA-sequencing analyses. This integrated analysis allows for assessing coordinated transcriptomic and metabolic responses in terms of both pathway enzyme expression and regulatory levels. Between two Pi availability treatments, a total of 155 metabolites differentially accumulated in soybean roots, of which were phosphorylated metabolites, flavonoids and amino acids. Meanwhile, a total of 1644 differentially expressed genes (DEGs) were identified in soybean roots, including 1199 up-regulated and 445 down-regulated genes. Integration of metabolome and transcriptome analyses revealed Pi starvation responsive connection between specific metabolic processes in soybean roots, especially metabolic processes involving phosphorylated metabolites (e.g., phosphorylated lipids and nucleic acids). Taken together, this study suggests that complex molecular responses scavenging internal Pi from phosphorylated metabolites are typical adaptive strategies soybean roots employ as responses to Pi starvation. Identified DEGs will provide potential target region for future efforts to develop P-efficient soybean cultivars.

An Integrative Systems Perspective on Plant Phosphate Research

The case for improving crop phosphorus-use-efficiency is widely recognized. Although much is known about the molecular and regulatory mechanisms, improvements have been hampered by the extreme complexity of phosphorus (P) dynamics, which involves soil chemistry; plant-soil interactions; uptake, transport, utilization and remobilization within plants; and agricultural practices. The urgency and direction of phosphate research is also dependent upon the finite sources of P, availability of stocks to farmers and reducing environmental hazards. This work introduces integrative systems approaches as a way to represent and understand this complexity, so that meaningful links can be established between genotype, environment, crop traits and yield. It aims to provide a large set of pointers to potential genes and research practice, with a view to encouraging members of the plant-phosphate research community to adopt such approaches so that, together, we can aid efforts in global food security.