OsSQD1 at the crossroads of phosphate and sulfur metabolism affects plant morphology and lipid composition in response to phosphate deprivation

The ZmNF-YC1-ZmAPRG pathway modulates low phosphorus tolerance in maize

Phosphorus (P) is an essential nutrient for plant growth and yield. Low phosphate use efficiency makes it important to clarify the molecular mechanism of low P stress. In our previous studies, a P efficiency gene ZmAPRG was identified. Here, we further screened the upstream regulator ZmNF-YC1 of ZmAPRG by yeast one hybrid (Y1H) assay, and found it was a low inorganic phosphorus (Pi)-inducible gene. The results of dual luciferase assays, expression analysis, and ChIP-qPCR assays showed that ZmNF-YC1 is a positive regulator of ZmAPRG. Overexpression of ZmNF-YC1 improved low P tolerance, whereas knockout of ZmNF-YC1 decreased low P tolerance in maize. Bimolecular fluorescence complementation (BiFC), yeast two hybrid (Y2H) assay, and yeast three hybrid (Y3H) assay further showed that ZmNF-YC1 can interact with ZmNF-YB14, and recruit ZmNF-YA4/10 to form NF-Y complexes. Transcriptional activation assay confirmed that the NF-Y complexes can activate the promoters of ZmAPRG. Meanwhile, transcriptome and metabolome analyses indicated that overexpression of ZmAPRG improves low P tolerance by regulating lipid composition and photosynthetic capacity, and chlorophyll fluorescence parameters provided evidence in support of this hypothesis. Furthermore, overexpression of ZmAPRG increased grain yield in inbred and hybrid maize under low P conditions. Taken together, our research revealed a low P tolerance mechanism of the ZmNF-YC1-ZmAPRG pathway.

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.

Arbuscular mycorrhizal fungi enhance phosphate uptake and alter bacterial communities in maize rhizosphere soil

Arbuscular mycorrhizal fungi (AMF) can symbiose with many plants and improve nutrient uptake for their host plant. Rhizosphere microorganisms have been pointed to play important roles in helping AMF to mobilize soil insoluble nutrients, especially phosphorus. Whether the change in phosphate transport under AMF colonization will affect rhizosphere microorganisms is still unknown. Here, we evaluated the links of interactions among AMF and the rhizosphere bacterial community of maize (Zea mays L.) by using a maize mycorrhizal defective mutant. Loss of mycorrhizal symbiosis function reduced the phosphorus concentration, biomass, and shoot length of maize colonized by AMF. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the bacterial community in the rhizosphere under AMF colonization. Further functional prediction based on amplicon sequencing indicated that rhizosphere bacteria involved in sulfur reduction were recruited by the AMF colonized mutant but reduced in the AMF- colonized wild type. These bacteria harbored much abundance of sulfur metabolism-related genes and negatively correlated with biomass and phosphorus concentrations of maize. Collectively, this study shows that AMF symbiosis recruited rhizosphere bacterial communities to improve soil phosphate mobilization, which may also play a potential role in regulating sulfur uptake. This study provides a theoretical basis for improving crop adaptation to nutrient deficiency through soil microbial management practices.

A stress-inducible protein regulates drought tolerance and flowering time in Brachypodium and Arabidopsis

To cope with environmental stresses and ensure maximal reproductive success, plants have developed strategies to adjust the timing of their transition to reproductive growth. This has a substantial impact on the stress resilience of crops and ultimately on agricultural productivity. Here, we report a previously uncharacterized, plant-specific gene family designated as Regulator of Flowering and Stress (RFS). Overexpression of the BdRFS gene in Brachypodium distachyon delayed flowering, increased biomass accumulation, and promoted drought tolerance, whereas clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated knockout mutants exhibited opposite phenotypes. A double T-DNA insertional mutant in the two Arabidopsis (Arabidopsis thaliana) homologs replicated the effects on flowering and water deprivation seen in the B. distachyon CRISPR knockout lines, highlighting the functional conservation of the family between monocots and dicots. Lipid analysis of B. distachyon and Arabidopsis revealed that digalactosyldiacylglycerol (DGDG) and phosphatidylcholine (PC) contents were significantly, and reciprocally, altered in overexpressor and knockout mutants. Importantly, alteration of C16:0-containing PC, a Flowering Locus T-interacting lipid, associated with flowering phenotype, with elevated levels corresponding to earlier flowering. Co-immunoprecipitation analysis suggested that BdRFS interacts with phospholipase Dα1 as well as several other abscisic acid-related proteins. Furthermore, reduction of C18:3 fatty acids in DGDG corresponded with reduced jasmonic acid metabolites in CRISPR mutants. Collectively, we suggest that stress-inducible RFS proteins represent a regulatory component of lipid metabolism that impacts several agronomic traits of biotechnological importance.

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.

Does Sulfoquinovosyl Diacylglycerol Synthase OsSQD1 Affect the Composition of Lipids in Rice Phosphate-Deprived Root?

Lipids are the essential components of the cell intracellular and plasma membranes. Sulfoquinovosyldiacylglycerol (SQDG) is a glycolipid; glycolipids can replace phospholipids in maintaining phosphate (Pi) homeostasis in plants which are undergoing Pi starvation. Sulfoquinovosyl diacylglycerol synthase 1 (OsSQD1) is a critical enzyme in the first step of catalyzation in the formation of SQDG in rice. In this study, the expression pattern of different zones in roots of OsSQD1 in response to different Pi conditions is examined, and it is found that OsSQD1 is highly expressed in lateral roots under Pi-sufficient and -deficient conditions. The root phenotype observation of different OsSQD1 transgenic lines suggests that the knockout/down of OsSQD1 inhibits the formation and growth of lateral roots under different Pi conditions. Additionally, the lipid concentrations in OsSQD1 transgenic line roots indicate that OsSQD1 knockout/down decreases the concentration of phospholipids and glycolipids in Pi-starved roots. The OsSQD1 mutation also changes the composition of different lipid species with different acyl chain lengths, mainly under Pi-deprived conditions. The relative transcript expression of genes relating to glycolipid synthesis and phospholipid degradation is estimated to help study the mechanism by which OsSQD1 exerts an influence on the alteration of lipid composition and concentration in Pi-starved roots. Moreover, in Pi-starved roots, the knockout of OsSQD1 decreases the unsaturated fatty acid content of phospholipids and glycolipids. To summarize, the present study demonstrates that OsSQD1 plays a key role in the maintenance of phospholipid and glycolipid composition in Pi-deprived rice roots, which may influence root growth and development under Pi-deprived conditions.

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.

Distribution of phenanthrene in the ospho2 reveals the involvement of phosphate on phenanthrene translocation and accumulation in rice

The intricate mechanisms involved in the acquisition and translocation of polycyclic aromatic hydrocarbons (PAHs) in plants have not been elucidated. Phosphate (Pi) is the bioavailable form of essential macronutrient phosphorus, which is acquired and subsequently assimilated for plant optimal growth and development. Rice phosphate overaccumulator 2 (OsPHO2) is a central constituent of the regulation of Pi homeostasis in rice. In the present study, the role of OsPHO2 in regulating the translocation and accumulation of phenanthrene (Phe) and the involvement of Pi in this process were investigated. The temporal study (1 d-35 d) revealed a significant and gradual increase of Phe accumulation in Pi-deprived roots of wild-type (WT) seedlings. Compared with the WT, the concentrations of Phe were significantly higher in the shoots of ospho2 (OsPHO2 mutant) grown hydroponically with Phe (1.5 mg/L) under +Pi (200 μM) and -Pi (10 μM) conditions. The sap experiment clearly showed the significant increases in levels of Phe in the xylem sap of ospho2 than the WT grown hydroponically with Phe and +Pi. Further, the concentrations of both Phe and P were coordinately higher in the culms and flag leaves of the mutants than WT at maturity in potting soil with LPhe (6 mg/kg) and HPhe (60 mg/kg). However, the concentrations of Phe in the seeds were comparable in the WT and mutants, suggesting a pivotal of OsPHO2 in attenuating Phe toxicity in the seed. In +Phe WT, the relative expression level of OsPHO2 in the shoots was significantly lower, while those of Pi transporters (PTs) OsPT4 and OsPT8 were significantly higher in the roots compared with -Phe. Together, the results provided evidence towards the involvement of Pi in OsPHO2-regulated translocation and accumulation of Phe in rice.

Transcriptome and Metabolome Analyses Revealed the Response Mechanism of Quinoa Seedlings to Different Phosphorus Stresses

Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous annual herb of Family Amaranthaceae and Subfamily Chenopodiaceae. It has high nutritional and economic value. Phosphorus (P) is an essential plant macronutrient, a component of many biomolecules, and vital to growth, development, and metabolism. We analyzed the transcriptomes and metabolomes of Dianli–1299 and Dianli–71 quinoa seedlings, compared their phenotypes, and elucidated the mechanisms of their responses to the phosphorus treatments. Phenotypes significantly varied with phosphorus level. The plants responded to changes in available phosphorus by modulating metabolites and genes implicated in glycerophospholipid, glycerolipid and glycolysis, and glyconeogenesis metabolism. We detected 1057 metabolites, of which 149 were differentially expressed (DEMs) and common to the control (CK) vs. the low-phosphorus (LP) treatment samples, while two DEMs were common to CK vs. the high-phosphorus (HP) treatment samples. The Kyoto Encyclopedia of genes and genomes (KEGG) annotated 29,232 genes, of which 231 were differentially expressed (DEGs) and common to CK vs. LP, while one was common to CK vs. HP. A total of 15 DEMs and 11 DEGs might account for the observed differences in the responses of the quinoa seedlings to the various phosphorus levels. The foregoing results may provide a theoretical basis for improving the phosphorus utilization efficiency in quinoa.

Sulfoquinovosyl diacylglycerol synthase 1 impairs glycolipid accumulation and photosynthesis in phosphate-deprived rice

Phosphate (Pi)-starved crops utilize phospholipids as a source for internal Pi supply by replacing non-phosphorus glycolipids. In rice, sulfoquinovosyl diacylglycerol synthase 1 (OsSQD1) functions as a key enzyme in the first step to catalyze sulfoquinovosyldiacylglycerol (SQDG) formation. Here we study differential expression of OsSQD1 in response to Pi, nitrogen, potassium, and iron-deficiencies in rice. Electrophoretic mobility shift assay suggested that OsSQD1 is regulated by OsPHR2 (Phosphate Starvation Response2), a MYB (v-myb avian myeloblastosis viral oncogene homolog) domain-containing transcription factor. The concentrations of different lipid species in ossqd1 knockout mutant demonstrated that OsSQD1 silencing increased the phospholipid content and altered fatty acid composition under Pi-deficiency. Moreover, OsSQD1 silencing reduces glycolipid accumulation under Pi-deficiency, and triggered the saturation of fatty acids in phospholipids and glycolipids treated with different Pi regimes. Relative amounts of transcripts related to phospholipid degradation and glycolipid synthesis were assessed to explore the mechanism by which OsSQD1 exerts an effect on lipid homeostasis under P-deficiency. Furthermore, OsSQD1 silencing inhibited photosynthesis, especially under Pi-deficient conditions, by down-regulating glycolipids in rice shoots. Taken together, our study reveals that OsSQD1 plays a key role in lipid homeostasis, especially glycolipid accumulation under Pi-deficiency, which results in the inhibition of photosynthesis.

Recent insights into the metabolic adaptations of phosphorus-deprived plants

Inorganic phosphate (Pi) is an essential macronutrient required for many fundamental processes in plants, including photosynthesis and respiration, as well as nucleic acid, protein, and membrane phospholipid synthesis. The huge use of Pi-containing fertilizers in agriculture demonstrates that the soluble Pi levels of most soils are suboptimal for crop growth. This review explores recent advances concerning the understanding of adaptive metabolic processes that plants have evolved to alleviate the negative impact of nutritional Pi deficiency. Plant Pi starvation responses arise from complex signaling pathways that integrate altered gene expression with post-transcriptional and post-translational mechanisms. The resultant remodeling of the transcriptome, proteome, and metabolome enhances the efficiency of root Pi acquisition from the soil, as well as the use of assimilated Pi throughout the plant. We emphasize how the up-regulation of high-affinity Pi transporters and intra- and extracellular Pi scavenging and recycling enzymes, organic acid anion efflux, membrane remodeling, and the remarkable flexibility of plant metabolism and bioenergetics contribute to the survival of Pi-deficient plants. This research field is enabling the development of a broad range of innovative and promising strategies for engineering phosphorus-efficient crops. Such cultivars are urgently needed to reduce inputs of unsustainable and non-renewable Pi fertilizers for maximum agronomic benefit and long-term global food security and ecosystem preservation.

Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum

BACKGROUND

Sulfur is a major component of biological molecules and thus an essential element for plants. Deficiency of sulfate, the main source of sulfur in soils, negatively influences plant growth and crop yield. The effect of sulfate deficiency on plants has been well characterized at the physiological, transcriptomic and metabolomic levels in Arabidopsis thaliana and a limited number of crop plants. However, we still lack a thorough understanding of the molecular mechanisms and regulatory networks underlying sulfate deficiency in most plants. In this work we analyzed the impact of sulfate starvation on the transcriptome of tomato plants to identify regulatory networks and key transcriptional regulators at a temporal and organ scale.

RESULTS

Sulfate starvation reduces the growth of roots and leaves which is accompanied by major changes in the organ transcriptome, with the response being temporally earlier in roots than leaves. Comparative analysis showed that a major part of the Arabidopsis and tomato transcriptomic response to sulfate starvation is conserved between these plants and allowed for the identification of processes specifically regulated in tomato at the transcript level, including the control of internal phosphate levels. Integrative gene network analysis uncovered key transcription factors controlling the temporal expression of genes involved in sulfate assimilation, as well as cell cycle, cell division and photosynthesis during sulfate starvation in tomato roots and leaves. Interestingly, one of these transcription factors presents a high identity with SULFUR LIMITATION1, a central component of the sulfate starvation response in Arabidopsis.

CONCLUSIONS

Together, our results provide the first comprehensive catalog of sulfate-responsive genes in tomato, as well as novel regulatory targets for future functional analyses in tomato and other crops.