Comparative proteome analyses of phosphorus responses in maize (Zea mays L.) roots of wild-type and a low-P-tolerant mutant reveal root characteristics associated with phosphorus efficiency

Unraveling the Mechanisms of Efficient Phosphorus Utilization in Popcorn (Zea mays L. var. everta): Insights from Proteomic and Metabolite Analysis

The expansion of agriculture and the need for sustainable practices drives breeders to develop plant varieties better adapted to abiotic stress such as nutrient deficiency, which negatively impacts yields. Phosphorus (P) is crucial for photosynthesis and plant growth, but its availability in the soil is often limited, hampering crop development. In this study, we examined the response of two popcorn inbred lines, L80 and P7, which have been characterized previously as P-use inefficient and P-use efficient, respectively, under low (stress) and high P (control) availability. Physiological measurements, proteomic analysis, and metabolite assays were performed to unravel the physiological and molecular responses associated with the efficient use of P in popcorn. We observed significant differences in protein abundances in response to the P supply between the two inbred lines. A total of 421 differentially expressed proteins (DEPs) were observed in L80 and 436 DEPs in P7. These proteins were involved in photosynthesis, protein biosynthesis, biosynthesis of secondary metabolites, and energy metabolism. In addition, flavonoids accumulated in higher abundance in P7. Our results help us understand the major components of P utilization in popcorn, providing new insights for popcorn molecular breeding programs.

A multi-omic survey of black cottonwood tissues highlights coordinated transcriptomic and metabolomic mechanisms for plant adaptation to phosphorus deficiency

Introduction

Phosphorus (P) deficiency in plants creates a variety of metabolic perturbations that decrease photosynthesis and growth. Phosphorus deficiency is especially challenging for the production of bioenergy feedstock plantation species, such as poplars (Populus spp.), where fertilization may not be practically or economically feasible. While the phenotypic effects of P deficiency are well known, the molecular mechanisms underlying whole-plant and tissue-specific responses to P deficiency, and in particular the responses of commercially valuable hardwoods, are less studied.

Methods

We used a multi-tissue and multi-omics approach using transcriptomic, proteomic, and metabolomic analyses of the leaves and roots of black cottonwood (Populus trichocarpa) seedlings grown under P-deficient (5 µM P) and replete (100 µM P) conditions to assess this knowledge gap and to identify potential gene targets for selection for P efficiency.

Results

In comparison to seedlings grown at 100 µM P, P-deficient seedlings exhibited reduced dry biomass, altered chlorophyll fluorescence, and reduced tissue P concentrations. In line with these observations, growth, C metabolism, and photosynthesis pathways were downregulated in the transcriptome of the P-deficient plants. Additionally, we found evidence of strong lipid remodeling in the leaves. Metabolomic data showed that the roots of P-deficient plants had a greater relative abundance of phosphate ion, which may reflect extensive degradation of P-rich metabolites in plants exposed to long-term P-deficiency. With the notable exception of the KEGG pathway for Starch and Sucrose Metabolism (map00500), the responses of the transcriptome and the metabolome to P deficiency were consistent with one another. No significant changes in the proteome were detected in response to P deficiency.

Discussion and conclusion

Collectively, our multi-omic and multi-tissue approach enabled the identification of important metabolic and regulatory pathways regulated across tissues at the molecular level that will be important avenues to further evaluate for P efficiency. These included stress-mediating systems associated with reactive oxygen species maintenance, lipid remodeling within tissues, and systems involved in P scavenging from the rhizosphere.

Proteomics reveals the significance of vacuole Pi transporter in the adaptability of Brassica napus to Pi deprivation

Vacuolar Pi transporters (VPTs) have recently been identified as important regulators of cellular Pi status in Arabidopsis thaliana and Oryza sativa. In the oil crop Brassica napus, BnA09PHT5;1a and BnC09PHT5;1a are two homologs of AtPHT5;1, the vacuolar Pi influx transporter in Arabidopsis. Here, we show that Pi deficiency induces the transcription of both homologs of PHT5;1a genes in B. napus leaves. Brassica PHT5;1a double mutants (DM) had smaller shoots and higher cellular Pi concentrations than wild-type (WT, Westar 10), suggesting the potential role of BnPHT5;1a in modulating cellular Pi status in B. napus. A proteomic analysis was performed to estimate the role of BnPHT5;1a in Pi fluctuation. Results show that Pi deprivation disturbs the abundance of proteins in the physiological processes involved in carbohydrate metabolism, response to stimulus and stress in B. napus, while disruption of BnPHT5;1a genes may exacerbate these processes. Besides, the processes of cell redox homeostasis, lipid metabolic and proton transmembrane transport are supposed to be unbalanced in BnPHT5;1a DM under the -Pi condition. Noteworthy, disruption of BnPHT5;1a genes severely alters the abundance of proteins related to ATP biosynthesis, and proton/inorganic cation transmembrane under normal Pi condition, which might contribute to B. napus growth limitations. Additionally, seven new protein markers of Pi homeostasis are identified in B. napus. Taken together, this study characterizes the important regulatory role of BnPHT5;1a genes as vacuolar Pi influx transporters in Pi homeostasis in B. napus.

Low phosphorus impact on Moso bamboo (Phyllostachys edulis) root morphological polymorphism and expression pattern of the related genes

Moso bamboo typically grows in phosphorus (P)-deficient soil that limits its growth and development. In this study, 10 Moso bamboo genotypes (Ph-1 to Ph-10) were evaluated for their responses to P deficiency during the seedling stage by growing them in both P-sufficient and P-deficient conditions. Adaptive responses to low P (LP) conditions were observed in the majority of genotypes. Under P deficiency conditions, the total biomass decreased in several genotypes, but at the same time, the root-to-shoot ratio increased. Principal component analysis identified two main comprehensive traits (PC1 and PC2) related to the root volume and surface area and P concentration and accumulation. Based on the analysis, two genotypes (Ph-6 and Ph-10) were identified with significantly different levels of tolerance to P deficiency. The results revealed that the genotype Ph-10 responded to P deficiency by significantly increasing the root surface area and volume, while simultaneously reducing the number of root cortex cells when compared with the genotype Ph-6, which showed the lowest tolerance (intolerant). The genotype Ph-10 exhibited a robust response to external LP conditions, marked by elevated expression levels of PHOSPHATE TRANSPORTERs and SYG1/PHO81/XPR1s. In situ Polymerase Chain Reaction (PCR) analysis also revealed distinct tissue-specific expression patterns of the genes in the roots, particularly highlighting the differences between Ph-6 and Ph-10. The results provide a foundation for elucidating the mechanism of LP tolerance, thus potentially contributing to developing high P-use efficiency in Moso bamboo species.

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.

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.

Comparative proteome analysis of phosphorus-responsive genotypes reveals the proteins differentially expressed under phosphorous starvation stress in rice

Phosphorus (P)-deficiency is one of the major nutrient constraints for global rice production. P-deficiency tolerance in rice involves complex regulatory mechanisms. To gain insights into the proteins involved in phosphorus acquisition and use efficiency in rice, proteome analysis of a high-yielding rice cultivar Pusa-44 and its near-isogenic line (NIL)-23 harboring a major phosphorous uptake (Pup1) QTL, grown under control and P-starvation stress, was performed. Comparative proteome profiling of shoot and root tissues from the plants grown hydroponically with P (16 ppm, +P) or without P (0 ppm, -P) resulted in the identification of 681 and 567 differentially expressed proteins (DEPs) in shoot of Pusa-44 and NIL-23, respectively. Similarly, 66 and 93 DEPs were identified in root of Pusa-44 and NIL-23, respectively. These P-starvation responsive DEPs were annotated to be involved in metabolic processes like photosynthesis, starch-, sucrose-, energy-metabolism, transcription factors (mainly ARF, ZFP, HD-ZIP, MYB), and phytohormone signaling. Comparative analysis of the expression patterns observed by proteome analysis with that reported at the transcriptome level indicated the Pup1 QTL-mediated post-transcriptional regulation plays an important role under -P stress. Thus, the present study describes the molecular aspect of the regulatory functions of Pup1 QTL under P-starvation stress in rice, which might help develop an efficient rice cultivar with enhanced P acquisition and assimilation for better performance in P-deficient soil.

Transcriptomics Insights into Phosphorus Stress Response of Myriophyllum aquaticum

Through excellent absorption and transformation, the macrophyte Myriophyllum (M.) aquaticum can considerably remove phosphorus from wastewater. The results of changes in growth rate, chlorophyll content, and roots number and length showed that M. aquaticum could cope better with high phosphorus stress compared with low phosphorus stress. Transcriptome and differentially expressed genes (DEGs) analyses revealed that, when exposed to phosphorus stresses at various concentrations, the roots were more active than the leaves, with more DEGs regulated. M. aquaticum also showed different gene expression and pathway regulatory patterns when exposed to low phosphorus and high phosphorus stresses. M. aquaticum's capacity to cope with phosphorus stress was maybe due to its improved ability to regulate metabolic pathways such as photosynthesis, oxidative stress reduction, phosphorus metabolism, signal transduction, secondary metabolites biosynthesis, and energy metabolism. In general, M. aquaticum has a complex and interconnected regulatory network that deals efficiently with phosphorus stress to varying degrees. This is the first time that the mechanisms of M. aquaticum in sustaining phosphorus stress have been fully examined at the transcriptome level using high-throughput sequencing analysis, which may indicate the direction of follow-up research and have some guiding value for its future applications.

Integrative physiological, transcriptome and metabolome analysis reveals the involvement of carbon and flavonoid biosynthesis in low phosphorus tolerance in cotton

Phosphorus (P) is an essential nutrient controlling plant growth and development through the regulation of basic metabolic processes; however, the molecular details of these pathways remain largely unknown. In this study, physiological, transcriptome, and metabolome analysis were compared for two cotton genotypes with different low P tolerance under P starvation and resupply. The results showed that the glucose, fructose, sucrose, and starch contents increased by 18.2%, 20.4%, 20.2%, and 14.3% in the roots and 18.3%, 23.3%, 11.0%, and 13.6% in the shoot of Jimian169 than DES926, respectively. Moreover, the activities of enzymes related to carbon and phosphorus metabolism were higher in the roots and shoots of Jimian169 than DES926. In addition, transcriptome analysis revealed that the number of differentially expressed genes (DEGs) was higher in both roots (830) and shoots (730) under P starvation and the DEGs drastically reduced upon P resupply. The KEGG analysis indicated that DEGs were mainly enriched in phenylpropanoid biosynthesis, carbon metabolism, and photosynthesis. The metabolome analysis showed the enrichment of phenylpropanoid, organic acids and derivatives, and lipids in all the pairs at a given time point. The combined transcriptome and metabolome analysis revealed that carbon metabolism and flavonoid biosynthesis are involved in the P starvation response in cotton. Moreover, co-expression network analysis identified 3 hub genes in the roots and shoots that regulate the pathways involved in the P starvation response. This study provides the foundation for understanding the mechanisms of low P tolerance and the hub genes as a potential target for the development of low P tolerant genotypes.

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.

Proteomic Analysis Dissects Molecular Mechanisms Underlying Plant Responses to Phosphorus Deficiency

Phosphorus (P) is an essential nutrient for plant growth. In recent decades, the application of phosphate (Pi) fertilizers has contributed to significant increases in crop yields all over the world. However, low efficiency of P utilization in crops leads to intensive application of Pi fertilizers, which consequently stimulates environmental pollution and exhaustion of P mineral resources. Therefore, in order to strengthen the sustainable development of agriculture, understandings of molecular mechanisms underlying P efficiency in plants are required to develop cultivars with high P utilization efficiency. Recently, a plant Pi-signaling network was established through forward and reverse genetic analysis, with the aid of the application of genomics, transcriptomics, proteomics, metabolomics, and ionomics. Among these, proteomics provides a powerful tool to investigate mechanisms underlying plant responses to Pi availability at the protein level. In this review, we summarize the recent progress of proteomic analysis in the identification of differential proteins that play roles in Pi acquisition, translocation, assimilation, and reutilization in plants. These findings could provide insights into molecular mechanisms underlying Pi acquisition and utilization efficiency, and offer new strategies in genetically engineering cultivars with high P utilization efficiency.

Transcriptome and metabolome analyses revealed the response mechanism of apple to different phosphorus stresses

Phosphorus (P) is an important element in numerous metabolic reactions and signalling pathways, but the molecular details of these pathways remain largely unknown. In this study, physiological, transcriptome and metabolite analyses of apple leaves and roots were compared under different P conditions. The results showed that different P stresses influenced phenotypic characteristics, soil plant analytical development (SPAD) values and the contents of flavonoids and anthocyanins in apple seedlings. The contents of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) and the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), acid phosphatase (ACP) and purple acid phosphatase (PAP) were also affected by different P stresses. In addition, RNA sequencing (RNA-seq) was used to characterize the influence of different P stresses on apple seedlings. Compared with control apple plants, there were 1246 and 1183 differentially expressed genes (DEGs) in leaves and roots under the low-P treatment and 60 and 1030 DEGs in leaves and roots under the high-P treatment, respectively. Gene Ontology (GO) analysis indicated that apple trees might change their responses to metabolic processes, cell proliferation, regulation of biological processes, reactive oxygen species metabolic processes and flavonoid metabolic processes under P stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further indicated that DEGs act on the mitogen-activated protein kinase (MAPK) signalling pathway, flavonoid biosynthesis, phenylpropanoid biosynthesis, and ATP-binding cassette (ABC) transporters. The metabolome analysis revealed that the levels of most amino acids and their derivatives, organic acids and flavonoids in roots treated with low-P stress were higher than those in roots of apple seedlings under control growth conditions. Apple seedlings regulate the flavonoid pathway to respond to different phosphorus environments. The results provide a framework for understanding the metabolic processes underlying different P responses and provide a foundation for improving the utilization efficiency of P in apple trees.

Genetic Dissection of Phosphorus Use Efficiency in a Maize Association Population under Two P Levels in the Field

Phosphorus (P) deficiency is an important challenge the world faces while having to increase crop yields. It is therefore necessary to select maize (Zea may L.) genotypes with high phosphorus use efficiency (PUE). Here, we extensively analyzed the biomass, grain yield, and PUE-related traits of 359 maize inbred lines grown under both low-P and normal-P conditions. A significant decrease in grain yield per plant and biomass, an increase in PUE under low-P condition, as well as significant correlations between the two treatments were observed. In a genome-wide association study, 49, 53, and 48 candidate genes were identified for eleven traits under low-P, normal-P conditions, and in low-P tolerance index (phenotype under low-P divided by phenotype under normal-P condition) datasets, respectively. Several gene ontology pathways were enriched for the genes identified under low-P condition. In addition, seven key genes related to phosphate transporter or stress response were molecularly characterized. Further analyses uncovered the favorable haplotype for several core genes, which is less prevalent in modern lines but often enriched in a specific subpopulation. Collectively, our research provides progress in the genetic dissection and molecular characterization of PUE in maize.

Phosphate and phosphite have a differential impact on the proteome and phosphoproteome of Arabidopsis suspension cell cultures

Phosphorus absorbed in the form of phosphate (H₂ PO₄^- ) is an essential but limiting macronutrient for plant growth and agricultural productivity. A comprehensive understanding of how plants respond to phosphate starvation is essential for the development of more phosphate-efficient crops. Here we employed label-free proteomics and phosphoproteomics to quantify protein-level responses to 48 h of phosphate versus phosphite (H₂ PO₃^- ) resupply to phosphate-deprived Arabidopsis thaliana suspension cells. Phosphite is similarly sensed, taken up and transported by plant cells as phosphate, but cannot be metabolized or used as a nutrient. Phosphite is thus a useful tool for differentiating between non-specific processes related to phosphate sensing and transport and specific responses to phosphorus nutrition. We found that responses to phosphate versus phosphite resupply occurred mainly at the level of protein phosphorylation, complemented by limited changes in protein abundance, primarily in protein translation, phosphate transport and scavenging, and central metabolism proteins. Altered phosphorylation of proteins involved in core processes such as translation, RNA splicing and kinase signaling was especially important. We also found differential phosphorylation in response to phosphate and phosphite in 69 proteins, including splicing factors, translation factors, the PHT1;4 phosphate transporter and the HAT1 histone acetyltransferase - potential phospho-switches signaling changes in phosphorus nutrition. Our study illuminates several new aspects of the phosphate starvation response and identifies important targets for further investigation and potential crop improvement.

Differential Gene Expression Responding to Low Phosphate Stress in Leaves and Roots of Maize by cDNA-SRAP

Phosphate (Pi) deficiency in soil can have severe impacts on the growth, development, and production of maize worldwide. In this study, a cDNA-sequence-related amplified polymorphism (cDNA-SRAP) transcript profiling technique was used to evaluate the gene expression in leaves and roots of maize under Pi stress for seven days. A total of 2494 differentially expressed fragments (DEFs) were identified in response to Pi starvation with 1202 and 1292 DEFs in leaves and roots, respectively, using a total of 60 primer pairs in the cDNA-SRAP analysis. These DEFs were categorized into 13 differential gene expression patterns. Results of sequencing and functional analysis showed that 63 DEFs (33 in leaves and 30 in roots) were annotated to a total of 54 genes involved in diverse groups of biological pathways, including metabolism, photosynthesis, signal transduction, transcription, transport, cellular processes, genetic information, and organismal system. This study demonstrated that (1) the cDNA-SRAP transcriptomic profiling technique is a powerful method to analyze differential gene expression in maize showing advantageous features among several transcriptomic methods; (2) maize undergoes a complex adaptive process in response to low Pi stress; and (3) a total of seven differentially expressed genes were identified in response to low Pi stress in leaves or roots of maize and could be used in the genetic modification of maize.

SH1-dependent maize seed development and starch synthesis via modulating carbohydrate flow and osmotic potential balance

BACKGROUND

As the main form of photoassimilates transported from vegetative tissues to the reproductive organs, sucrose and its degradation products are crucial for cell fate determination and development of maize kernels. Despite the relevance of sucrose synthase SH1 (shrunken 1)-mediated release of hexoses for kernel development, the underlying physiological and molecular mechanisms are not yet well understood in maize (Zea mays).

RESULTS

Here, we identified a new allelic mutant of SH1 generated by EMS mutagenesis, designated as sh1*. The mutation of SH1 caused more than 90% loss of sucrose synthase activity in sh1* endosperm, which resulted in a significant reduction in starch contents while a dramatic increase in soluble sugars. As a result, an extremely high osmolality in endosperm cells of sh1* was generated, which caused kernel swelling and affected the seed development. Quantitative measurement of phosphorylated sugars showed that Glc-1-P in endosperm of sh1* (17 μg g^- 1 FW) was only 5.2% of that of wild-type (326 μg g^- 1 FW). As a direct source of starch synthesis, the decrease of Glc-1-P may cause a significant reduction in carbohydrates that flow to starch synthesis, ultimately contributing to the defects in starch granule development and reduction of starch content.

CONCLUSIONS

Our results demonstrated that SH1-mediated sucrose degradation is critical for maize kernel development and starch synthesis by regulating the flow of carbohydrates and maintaining the balance of osmotic potential.

Metabolic alterations provide insights into Stylosanthes roots responding to phosphorus deficiency

BACKGROUND

Phosphorus (P) deficiency is one of the major constraints limiting plant growth, especially in acid soils. Stylosanthes (stylo) is a pioneer tropical legume with excellent adaptability to low P stress, but its underlying mechanisms remain largely unknown.

RESULTS

In this study, the physiological, molecular and metabolic changes in stylo responding to phosphate (Pi) starvation were investigated. Under low P condition, the growth of stylo root was enhanced, which was attributed to the up-regulation of expansin genes participating in root growth. Metabolic profiling analysis showed that a total of 256 metabolites with differential accumulations were identified in stylo roots response to P deficiency, which mainly included flavonoids, sugars, nucleotides, amino acids, phenylpropanoids and phenylamides. P deficiency led to significant reduction in the accumulation of phosphorylated metabolites (e.g., P-containing sugars, nucleotides and cholines), suggesting that internal P utilization was enhanced in stylo roots subjected to low P stress. However, flavonoid metabolites, such as kaempferol, daidzein and their glycoside derivatives, were increased in P-deficient stylo roots. Furthermore, the qRT-PCR analysis showed that a set of genes involved in flavonoids synthesis were found to be up-regulated by Pi starvation in stylo roots. In addition, the abundances of phenolic acids and phenylamides were significantly increased in stylo roots during P deficiency. The increased accumulation of the metabolites in stylo roots, such as flavonoids, phenolic acids and phenylamides, might facilitate P solubilization and cooperate with beneficial microorganisms in rhizosphere, and thus contributing to P acquisition and utilization in stylo.

CONCLUSIONS

These results suggest that stylo plants cope with P deficiency by modulating root morphology, scavenging internal Pi from phosphorylated metabolites and increasing accumulation of flavonoids, phenolic acids and phenylamides. This study provides valuable insights into the complex responses and adaptive mechanisms of stylo roots to P deficiency.

Metabolite profiling and genome-wide association studies reveal response mechanisms of phosphorus deficiency in maize seedling

Inorganic phosphorus (Pi) is an essential element in numerous metabolic reactions and signaling pathways, but the molecular details of these pathways remain largely unknown. In this study, metabolite profiles of maize (Zea mays L.) leaves and roots were compared between six low-Pi-sensitive lines and six low-Pi-tolerant lines under Pi-sufficient and Pi-deficient conditions to identify pathways and genes associated with the low-Pi stress response. Results showed that under Pi deprivation the concentrations of nucleic acids, organic acids and sugars were increased, but that the concentrations of phosphorylated metabolites, certain amino acids, lipid metabolites and nitrogenous compounds were decreased. The levels of secondary metabolites involved in plant immune reactions, including benzoxazinoids and flavonoids, were significantly different in plants grown under Pi-deficient conditions. Among them, the 11 most stable metabolites showed significant differences under low- and normal-Pi conditions based on the coefficient of variation (CV). Isoleucine and alanine were the most stable metabolites for the identification of Pi-sensitive and Pi-resistant maize inbred lines. With the significant correlation between morphological traits and metabolites, five low-Pi-responding consensus genes associated with morphological traits and simultaneously involved in metabolic pathways were mined by combining metabolites profiles and genome-wide association study (GWAS). The consensus genes induced by Pi deficiency in maize seedlings were also validated by reverse-transcription quantitative polymerase chain reaction (RT-qPCR). Moreover, these genes were further validated in a recombinant inbred line (RIL) population, in which the glucose-6-phosphate-1-epimerase encoding gene mediated yield and correlated traits to phosphorus availability. Together, our results provide a framework for understanding the metabolic processes underlying Pi-deficient responses and give multiple insights into improving the efficiency of Pi use in maize.

Comparative Study Reveals Insights of Sheepgrass (Leymus chinensis) Coping With Phosphate-Deprived Stress Condition

Sheepgrass [Leymus chinensis (Trin.) Tzvel] is a valuable forage plant highly significant to the grassland productivity of Euro-Asia steppes. Growth of above-ground tissues of L. chinensis is the major component contributing to the grass yield. Although it is generally known that this species is sensitive to ecosystem disturbance and adverse environments, detailed information of how L. chinensis coping with various nutrient deficiency especially phosphate deprivation (-Pi) is still limited. Here, we investigated impact of Pi-deprivation on shoot growth and biomass accumulation as well as photosynthetic properties of L. chinensis. Growth inhibition of Pi-deprived seedlings was most obvious and reduction of biomass accumulation and net photosynthetic rate (Pn) was 55.3 and 63.3%, respectively, compared to the control plants grown under Pi-repleted condition. Also, we compared these characters with seedlings subjected to low-Pi stress condition. Pi-deprivation caused 18.5 and 12.3% more reduction of biomass and Pn relative to low-Pi-stressed seedlings, respectively. Further analysis of in vivo chlorophyll fluorescence and thylakoid membrane protein complexes using 2D-BN/SDS-PAGE combined with immunoblot detection demonstrated that among the measured photosynthetic parameters, decrease of ATP synthase activity was most pronounced in Pi-deprived plants. Together with less extent of lipid peroxidation of the thylakoid membranes and increased ROS scavenger enzyme activities in the leaves of Pi-deprived seedlings, we suggest that the decreased activity of ATP synthase in their thylakoids is the major cause of the greater reduction of photosynthetic efficiency than that of low-Pi stressed plants, leading to the least shoot growth and biomass production in L. chinensis.

Physiological and quantitative proteomic analyses unraveling potassium deficiency stress response in alligator weed (Alternanthera philoxeroides L.) root

Physiological and iTRAQ based proteomic analysis provided new insights into potassium deficiency stress response in alligator weed root. Alligator weed (Alternanthera philoxeroides) has a strong ability to adapt to potassium deficiency (LK) stress. Proteomic changes in response to this stress are largely unknown in alligator weed. In this study, we investigated physiological and molecular mechanisms under LK using isobaric tags for relative and absolute quantitation to characterize proteome-level changes in this plant. First, root physiology, 2, 3, 5-Triphenyl-trazolium chloride (TTC) assay and peroxidase activity were significantly altered after 10 and 15 days of LK treatment. The comparative proteomic analysis suggested a total of 375 proteins were differential abundance proteins. The proteomic results were verified by western blot assays and quantitative real-time PCR. Correlation analysis of transcription and proteomics suggested protein processing in the endoplasmic reticulum, endocytosis, and spliceosome pathways were significantly enriched. The protein responsible for energy metabolism, signal sensing and transduction and protein degradation played crucial roles in this stress. Twelve ubiquitin pathway related proteins were identified in our study, among them 11 proteins were up-regulated. All protein ubiquitination of lysine using pan antibodies were also increased after LK treatment. Our study provide a valuable insights of molecular mechanism underlying LK stress response in alligator weed roots and afford a vital basis to further study potassium nutrition molecular breeding of other plant species.

Comparative Analysis of Soybean Root Proteome Reveals Molecular Basis of Differential Carboxylate Efflux under Low Phosphorus Stress

Carboxylate efflux from roots is a crucial and differential response of soybean genotypes to low phosphorus (P) stress. Exudation of carboxylic acids including oxalate, citrate, succinate and fumarate was induced under low P stress, particularly in P-efficient soybean genotypes. Enhancement of root length, surface area and volume further improved P acquisition under low P stress. To understand the molecular basis of carboxylate efflux under low P stress, the root proteome of contrasting genotypes (P-efficient: EC-232019 and P-inefficient: EC-113396) was compared. Among a total of 325 spots, 105 (32%) were differentially abundant proteins (DAPs) between sufficient (250 µM) and low P (4 µM) levels. Abundance of 44 (14%) proteins decreased by more than two-fold under low P stress, while 61 (19%) proteins increased by more than two-fold. Protein identification and annotation revealed that the DAPs were involved in a myriad of functions including carboxylic acid synthesis, carbohydrate, protein and lipid metabolism. Proteins with significant abundance included malate dehydrogenase, isocitrate dehydrogenase, phosphoglucomutase, phosphoglycerate mutase, fructokinase, enolase, phosphoglycerate kinase, triosephosphate isomerase, alcohol dehydrogenase, glucan water dikinase, glutamine synthetase and argininosuccinate lyase. Inferences from proteomic analysis suggests the crosstalk between various metabolic pathways implicated in conferring superior P acquisition efficiency under stress.

Highly Efficient Single-Step Enrichment of Low Abundance Phosphopeptides from Plant Membrane Preparations

Mass spectrometry (MS)-based large scale phosphoproteomics has facilitated the investigation of plant phosphorylation dynamics on a system-wide scale. However, generating large scale data sets for membrane phosphoproteins usually requires fractionation of samples and extended hands-on laboratory time. To overcome these limitations, we developed "ShortPhos," an efficient and simple phosphoproteomics protocol optimized for research on plant membrane proteins. The optimized workflow allows fast and efficient identification and quantification of phosphopeptides, even from small amounts of starting plant materials. "ShortPhos" can produce label-free datasets with a high quantitative reproducibility. In addition, the "ShortPhos" protocol recovered more phosphorylation sites from membrane proteins, especially plasma membrane and vacuolar proteins, when compared to our previous workflow and other membrane-based data in the PhosPhAt 4.0 database. We applied "ShortPhos" to study kinase-substrate relationships within a nitrate-induction experiment on Arabidopsis roots. The "ShortPhos" identified significantly more known kinase-substrate relationships compared to previous phosphoproteomics workflows, producing new insights into nitrate-induced signaling pathways.

Identifying the Genes Regulated by AtWRKY6 Using Comparative Transcript and Proteomic Analysis under Phosphorus Deficiency

Phosphorus (P) is an important mineral nutrient for plant growth and development. Overexpressing AtWRKY6 (35S:WRKY6-9) was more sensitive and wrky6 (wrky6-1) was more resistant under low Pi conditions. To better understand the function of AtWRKY6 under low phosphate stress conditions, we applied two-dimensional gel electrophoresis (2-DE) to analyse differentially expressed proteins in the shoots and roots between wild type, 35S:WRKY6-9 and wrky6-1 after phosphorus deficiency treatment for three days. The results showed 88 differentially abundant protein spots, which were identified between the shoots and roots of 35S:WRKY6-9 and wrky6-1 plants. In addition, 59 differentially expressed proteins were identified in the leaves and roots of 35S:WRKY6-9 plants. After analysis, 9 genes with W-box elements in their promoter sequences were identified in the leaves, while 6 genes with W-box elements in their promoter sequences were identified in the roots. A total of 8 genes were identified as potential target genes according to the quantitative PCR (QPCR) and two dimension difference gel electrophoresis, (2D-DIGE) results, including ATP synthase, gln synthetase, nitrilase, 14-3-3 protein, carbonic anhydrases 2, and tryptophan synthase. These results provide important information concerning the AtWRKY6 regulation network and reveal potential vital target genes of AtWRKY6 under low phosphorus stress. two dimension difference gel electrophoresis, 2D-DIGE.

Identification of the differentially accumulated proteins associated with low phosphorus tolerance in a Tibetan wild barley accession

Low phosphorus (LP) in soil is a widely-occurred limiting factor for crop production in the world. In a previous study we identified a highly LP-tolerant Tibetan wild barley accession (XZ99). Here, a comparatively proteomic analysis was conducted using three barley genotypes differing in LP tolerance to reveal the mechanisms underlying the LP tolerance of XZ99. Totally, 31 differentially accumulated proteins were identified in the roots and leaves of the three genotypes using 2-dimensional gel electrophoresis coupled with mass spectrometry. They were involved in the various biological processes, including carbon and energy metabolism, signal transduction, cell growth and division, secondary metabolism, and stress defense. In comparison with XZ100 (LP sensitive) and ZD9 (LP moderately-tolerant), XZ99 had a more developed root system, which is mainly attributed to enhanced carbohydrate metabolizing proteins under LP conditions. The current results showed that Tibetan wild barley XZ99 and cultivated barley cultivar ZD9 differ in the mechanism of LP tolerance. The changes of the proteins associated with carbohydrate metabolism could account for the difference between the LP-tolerant and LP-sensitive genotypes. In addition, the mRNA expression levels of 9 LP responsive proteins were verified by qRT-PCR. The current results may open a new avenue of understanding the LP tolerance in plants on the proteomic basis.

Proteomic Analysis Provides New Insights in Phosphorus Homeostasis Subjected to Pi (Inorganic Phosphate) Starvation in Tomato Plants (Solanum lycopersicum L.)

Phosphorus is a major nutrient acquired by plants via high-affinity inorganic phosphate (Pi) transporters. To determine the adaptation and homeostasis strategy to Pi starvation, we compared the proteome analysis of tomato leaves that were treated with and without Pi (as KH2PO4) for 10 days. Among 600 reproducible proteins on 2-DE gels 46 of them were differentially expressed. These proteins were involved in major metabolic pathways, including photosynthesis, transcriptional/translational regulations, carbohydrate/energy metabolism, protein synthesis, defense response, and other secondary metabolism. The results also showed that the reduction in photosynthetic pigments lowered P content under -Pi treatments. Furthermore, high-affinity Pi transporters (lePT1 and lePT2) expressed in higher amounts under -Pi treatments. Also, the accumulation of Pi transporters was observed highly in the epidermis and palisade parenchyma under +Pi treatments compared to -Pi treatments. Our data suggested that tomato plants developed reactive oxygen species (ROS) scavenging mechanisms to cope with low Pi content, including the up-regulation of proteins mostly involved in important metabolic pathways. Moreover, Pi-starved tomato plants increased their internal Pi utilization efficiency by increasing the Pi transporter genes and their rational localization. These results thus provide imperative information about how tomato plants respond to Pi starvation and its homeostasis.

Polymorphisms in the AOX2 gene are associated with the rooting ability of olive cuttings

Different rooting ability candidate genes were tested on an olive cross progeny. Our results demonstrated that only the AOX2 gene was strongly induced. OeAOX2 was fully characterised and correlated to phenotypical traits. The formation of adventitious roots is a key step in the vegetative propagation of trees crop species, and this ability is under strict genetic control. While numerous studies have been carried out to identify genes controlling adventitious root formation, only a few loci have been characterised. In this work, candidate genes that were putatively involved in rooting ability were identified in olive (Olea europaea L.) by similarity with orthologs identified in other plant species. The mRNA levels of these genes were analysed by real-time PCR during root induction in high- (HR) and low-rooting (LR) individuals. Interestingly, alternative oxidase 2 (AOX2), which was previously reported to be a functional marker for rooting in olive cuttings, showed a strong induction in HR individuals. From the OeAOX2 full-length gene, alleles and effective polymorphisms were distinguished and analysed in the cross progeny, which were segregated based on rooting. The results revealed a possible correlation between two single nucleotide polymorphisms of OeAOX2 gene and rooting ability.

Proteomic and comparative genomic analysis reveals adaptability of Brassica napus to phosphorus-deficient stress

Given low solubility and immobility in many soils of the world, phosphorus (P) may be the most widely studied macronutrient for plants. In an attempt to gain an insight into the adaptability of Brassica napus to P deficiency, proteome alterations of roots and leaves in two B. napus contrasting genotypes, P-efficient 'Eyou Changjia' and P-inefficient 'B104-2', under long-term low P stress and short-term P-free starvation conditions were investigated, and proteomic combined with comparative genomic analyses were conducted to interpret the interrelation of differential abundance protein species (DAPs) responding to P deficiency with quantitative trait loci (QTLs) for P deficiency tolerance. P-efficient 'Eyou Changjia' had higher dry weight and P content, and showed high tolerance to low P stress compared with P-inefficient 'B104-2'. A total of 146 DAPs were successfully identified by MALDI TOF/TOF MS, which were categorized into several groups including defense and stress response, carbohydrate and energy metabolism, signaling and regulation, amino acid and fatty acid metabolism, protein process, biogenesis and cellular component, and function unknown. 94 of 146 DAPs were mapped to a linkage map constructed by a B. napus population derived from a cross between the two genotypes, and 72 DAPs were located in the confidence intervals of QTLs for P efficiency related traits. We conclude that the identification of these DAPs and the co-location of DAPs with QTLs in the B. napus linkage genetic map provide us novel information in understanding the adaptability of B. napus to P deficiency, and helpful to isolate P-efficient genes in B. napus.

BIOLOGICAL SIGNIFICANCE

Low P seriously limits the production and quality of B. napus. Proteomics and genetic linkage map were widely used to study the adaptive strategies of B. napus response to P deficiency, proteomic combined with comparative genetic analysis to investigate the correlations between DAPs and QTLs are scarce. Thus, we herein investigated proteome alteration of the roots and leaves in two B. napus genotypes, with different P-deficient tolerances, in response to long-term low P stress and short-term P-free starvation by 2-DE. And comparative genomic was conducted to map the DAPs to the linkage map of B. napus by sequence alignment. The present study offers new insights into adaptability mechanism of B. napus to P deficiency and provides novel information in map-based cloning to isolate the genes in B. napus and scientific improvement of P-efficient in practice.

Dissecting the transcriptional response to elicitors in Vitis vinifera cells

The high effectiveness of cyclic oligosaccharides like cyclodextrins in the production of trans-resveratrol in Vitis vinifera cell cultures is enhanced in the presence of methyl jasmonate. In order to dissect the basis of the interactions among the elicitation responses triggered by these two compounds, a transcriptional analysis of grapevine cell cultures treated with cyclodextrins and methyl jasmonate separately or in combination was carried out. The results showed that the activation of genes encoding enzymes from phenylpropanoid and stilbene biosynthesis induced by cyclodextrins alone was partially enhanced in the presence of methyl jasmonate, which correlated with their effects on trans-resveratrol production. In addition, protein translation and cell cycle regulation were more highly repressed in cells treated with cyclodextrins than in those treated with methyl jasmonate, and this response was enhanced in the combined treatment. Ethylene signalling was activated by all treatments, while jasmonate signalling and salicylic acid conjugation were activated only in the presence of methyl jasmonate and cyclodextrins, respectively. Moreover, the combined treatment resulted in a crosstalk between the signalling cascades activated by cyclodextrins and methyl jasmonate, which, in turn, provoked the activation of additional regulatory pathways involving the up-regulation of MYB15, NAC and WRKY transcription factors, protein kinases and calcium signal transducers. All these results suggest that both elicitors cause an activation of the secondary metabolism in detriment of basic cell processes like the primary metabolism or cell division. Crosstalk between cyclodextrins and methyl jasmonate-induced signalling provokes an intensification of these responses resulting in a greater trans-resveratrol production.

Phosphoproteome and proteome analyses reveal low-phosphate mediated plasticity of root developmental and metabolic regulation in maize (Zea mays L.)

Phosphate (Pi) deficiency has become a significant challenge to worldwide agriculture due to the depletion of accessible rock phosphate that is the major source of cheap Pi fertilizers. Previous research has identified a number of diverse adaptive responses to Pi starvation in the roots of higher plants. In this study, we found that accelerated axile root elongation of Pi-deprived maize plants resulted from enhanced cell proliferation. Comparative phosphoproteome and proteome profiles of maize axile roots were conducted in four stages in response to Pi deficiency by multiplex staining of high-resolution two dimensional gel separated proteins. Pro-Q DPS stained gels revealed that 6% of phosphoprotein spots displayed changes in phosphorylation state following low-Pi treatment. These proteins were involved in a large number of metabolic and cellular pathways including carbon metabolism and signal transduction. Changes in protein abundance of a number of enzymes indicated that low-Pi induced a number of carbon flux modifications in metabolic processes including sucrose breakdown and other downstream sugar metabolic pathways. A few key metabolic enzymes, including sucrose synthase (EC 2.4.1.13) and malate dehydrogenase (EC 1.1.1.37), and several signaling components involved in protein kinase or phosphatase cascades, auxin signaling and 14-3-3 proteins displayed low-Pi responsive changes in phosphorylation state or protein abundance. A variety of key enzymes and signaling components identified as potential targets for phosphorylation provide novel clues for comprehensive understanding of Pi regulation in plants. Protein phosphorylation, coordinating with changes in protein abundance, is required for maize root metabolic regulation and developmental acclimation to Pi starvation.

Root architecture and root and tuber crop productivity

It is becoming increasingly evident that optimization of root architecture for resource capture is vital for enabling the next green revolution. Although cereals provide half of the calories consumed by humans, root and tuber crops are the second major source of carbohydrates globally. Yet, knowledge of root architecture in root and tuber species is limited. In this opinion article, we highlight what is known about the root system in root and tuber crops, and mark new research directions towards a better understanding of the relation between root architecture and yield. We believe that unraveling the role of root architecture in root and tuber crop productivity will improve global food security, especially in regions with marginal soil fertility and low-input agricultural systems.

Comparative proteome analysis of the response of ramie under N, P and K deficiency

Ramie is an important natural fiber. There has been little research on the molecular mechanisms of ramie related to the absorption, utilization and metabolism of nitrogen (N), phosphorus (P) and potassium (K). One approach to reveal the mechanisms of N, P and K (NPK) utilization and metabolism in ramie is comparative proteome analysis. The differentially expressed proteins in the leaves of ramie were analyzed by proteome analysis after 6 days of N- and K-deficient treatments and 3 days of P-deficient treatment using MALDI-TOF/TOF mass spectrometry and 32, 27 and 51 differential proteins were obtained, respectively. These proteins were involved in photosynthesis, protein destination and storage, energy metabolism, primary metabolism, disease/defense, signal transduction, cell structure, transcription, secondary metabolism and protein synthesis. Ramie responded to NPK stress by enhancing secondary metabolism and reducing photosynthesis and energy metabolism to increase endurance. Specifically, ramie adapted to NPK deficiency by increasing signal transduction pathways, enhancing the connection between glycolysis and photosynthesis, promoting the intracellular flow of carbon and N; promoting the synthesis cysteine and related hormones and upregulating actin protein to promote growth of the root system. The experimental results provide important information for further study on the high-efficiency NPK utilization mechanism of ramie.

Comparative proteomic analyses provide new insights into low phosphorus stress responses in maize leaves

Phosphorus deficiency limits plant growth and development. To better understand the mechanisms behind how maize responds to phosphate stress, we compared the proteome analysis results of two groups of maize leaves that were treated separately with 1,000 µM (control, +P) and 5 µM of KH2PO4 (intervention group, -P) for 25 days. In total, 1,342 protein spots were detected on 2-DE maps and 15.43% had changed (P<0.05; ≥1.5-fold) significantly in quantity between the +P and -P groups. These proteins are involved in several major metabolic pathways, including photosynthesis, carbohydrate metabolism, energy metabolism, secondary metabolism, signal transduction, protein synthesis, cell rescue and cell defense and virulence. The results showed that the reduction in photosynthesis under low phosphorus treatment was due to the down-regulation of the proteins involved in CO2 enrichment, the Calvin cycle and the electron transport system. Electron transport and photosynthesis restrictions resulted in a large accumulation of peroxides. Maize has developed many different reactive oxygen species (ROS) scavenging mechanisms to cope with low phosphorus stress, including up-regulating its antioxidant content and antioxidase activity. After being subjected to phosphorus stress over a long period, maize may increase its internal phosphorus utilization efficiency by altering photorespiration, starch synthesis and lipid composition. These results provide important information about how maize responds to low phosphorus stress.

Identification and comparative analysis of low phosphate tolerance-associated microRNAs in two maize genotypes

Low phosphate (Pi) availability is a major constraint on maize growth and productivity. MicroRNAs (miRNAs) are known to play critical roles in plant responses to various environmental conditions. The identification of low Pi tolerance-associated miRNAs will accelerate the development of Pi starvation tolerant maize plants. However, miRNAs associated with low Pi tolerance have not been identified. In this study, we compared deep sequencing small RNA reads from two maize genotypes, the wild type, Qi319, and the low Pi tolerant mutant, 99038, under normal and low Pi conditions. Six known miRNA families and seven novel miRNAs were found differently expressed by the two genotypes. All these miRNAs were confirmed by sequencing a second batch of small RNA libraries constructed in the same way as those used in the first sequencing. The expression profiles of some of these miRNAs were further confirmed by real-time PCR. The predicted target genes of the low Pi tolerance-associated miRNAs were involved in root development or stress responses. Expression levels of some of target genes were significantly different between Qi319 and 99038. These findings suggested that miRNAs may play important roles in low Pi tolerance in maize and may be a key factor in determining the level of low Pi tolerance in different maize genotypes. This study provides an approach for identifying low Pi tolerance-associated miRNAs and can help in the selection and manipulation of high performing maize genotypes under low Pi conditions.

Proteomics dissection of plant responses to mineral nutrient deficiency

Plants require at least 17 essential nutrients to complete their life cycle. Except for carbon, hydrogen, and oxygen, other essential nutrients are mineral nutrients, which are mainly acquired from soils by roots. In natural soils, the availability of most essential mineral nutrients is very low and hard to meet the demand of plants. Developing crops with high nutrient efficiency is essential for sustainable agriculture, which requires more understandings of crop responses to mineral nutrient deficiency. Proteomic techniques provide a crucial and complementary tool to dissect molecular mechanisms underlying crop adaptation to mineral nutrient deficiency in the rapidly processing postgenome era. This review gives a comparative overview about identification of mineral nutrient deficiency responsive proteins using proteomic analysis, and discusses the current status for crop proteomics and its challenges to be integrated into systems biology approaches for developing crops with high mineral nutrient efficiency.

Approaches towards nitrogen- and phosphorus-efficient rice

BACKGROUND AND AIMS

Food production has to increase to meet the demand of a growing population. In light of the high energy costs and increasingly scarce resources, future agricultural systems have to be more productive and more efficient in terms of inputs such as fertilizer and water. The development of rice varieties with high yield under low-nutrient conditions has therefore become a breeding priority. The rapid progress made in sequencing and molecular-marker technology is now beginning to change the way breeding is done, providing new opportunities.

SCOPE

Nitrogen (N) and phosphorus (P) are applied to agricultural systems in large quantities and a deficiency of either nutrient leads to yield losses and triggers complex molecular and physiological responses. The underlying genes are now being identified and studied in detail, and an increasing number of quantitative trait loci (QTLs) related to N and P uptake and utilization are being reported. Here, we provide an overview of the different aspects related to N and P in rice production systems, and apply a breeder's perspective on the potential of relevant genes and pathways for breeding applications.

MAIN POINTS

For the development of nutrient-efficient rice, a holistic approach should be followed combining optimized fertilizer management with enhanced nutrient uptake via a vigorous root system, leading to increased grain filling and yield. Despite an increasing number of N- and P-related genes and QTLs being reported, very few are actively used in molecular breeding programmes. The complex regulation of N- and P-related pathways challenges breeders and the research community to identify large-effect genes/QTLs. For this it will be important to focus more on the analysis of tolerant genotypes rather than model plants, since tolerance pathways may employ a different set of genes.

Phosphate starvation of maize inhibits lateral root formation and alters gene expression in the lateral root primordium zone

BACKGROUND

Phosphorus (P) is an essential macronutrient for all living organisms. Maize (Zea mays) is an important human food, animal feed and energy crop throughout the world, and enormous quantities of phosphate fertilizer are required for maize cultivation. Thus, it is important to improve the efficiency of the use of phosphate fertilizer for maize.

RESULTS

In this study, we analyzed the maize root response to phosphate starvation and performed a transcriptomic analysis of the 1.0-1.5 cm lateral root primordium zone. In the growth of plants, the root-to-shoot ratio (R/L) was reduced in both low-phosphate (LP) and sufficient-phosphate (SP) solutions, but the ratio (R/L) exhibited by the plants in the LP solution was higher than that of the SP plants. The growth of primary roots was slightly promoted after 6 days of phosphate starvation, whereas the numbers of lateral roots and lateral root primordia were significantly reduced, and these differences were increased when associated with the stress caused by phosphate starvation. Among the results of a transcriptomic analysis of the maize lateral root primordium zone, there were two highlights: 1) auxin signaling participated in the response and the modification of root morphology under low-phosphate conditions, which may occur via local concentration changes due to the biosynthesis and transport of auxin, and LOB domain proteins may be an intermediary between auxin signaling and root morphology; and 2) the observed retardation of lateral root development was the result of co-regulation of DNA replication, transcription, protein synthesis and degradation and cell growth.

CONCLUSIONS

These results indicated that maize roots show a different growth pattern than Arabidopsis under low-phosphate conditions, as the latter species has been observed to halt primary root growth when the root tip comes into contact with low-phosphate media. Moreover, our findings enrich our understanding of plant responses to phosphate deficits and of root morphogenesis in maize.

A novel rice gene, NRR responds to macronutrient deficiency and regulates root growth

To better understand the response of rice to nutrient stress, we have taken a systematic approach to identify rice genes that respond to deficiency of macronutrients and affect rice growth. We report here the expression and biological functions of a previously uncharacterized rice gene that we have named NRR (nutrition response and root growth). NRR is alternatively spliced, producing two 5'-coterminal transcripts, NRRa and NRRb, encoding two proteins of 308 and 223 aa, respectively. Compared to NRRb, NRRa possesses an additional CCT domain at the C-terminus. Expression of NRR in rice seedling roots was significantly influenced by deficiency of macronutrients. Knock-down of expression of NRRa or NRRb by RNA interference resulted in enhanced rice root growth. By contrast, overexpression of NRRa in rice exhibited significantly retarded root growth. These results revealed that both NRRa and NRRb played negative regulatory roles in rice root growth. Our findings suggest that NRRa and NRRb, acting as the key components, modulate the rice root architecture with the availability of macronutrients.

Arbuscular mycorrhizal symbiosis elicits proteome responses opposite of P-starvation in SO4 grapevine rootstock upon root colonisation with two Glomus species

Although plant biotisation with arbuscular mycorrhizal fungi (AMF) is a promising strategy for improving plant health, a better knowledge regarding the molecular mechanisms involved is required. In this context, we sought to analyse the root proteome of grapevine rootstock Selection Oppenheim 4 (SO4) upon colonisation with two AMF. As expected, AMF colonisation stimulates plant biomass. At the proteome level, changes in protein amounts due to AMF colonisation resulted in 39 differentially accumulated two-dimensional electrophoresis spots in AMF roots relative to control. Out of them, 25 were co-identified in SO4 roots upon colonisation by Glomus irregulare and Glomus mosseae supporting the existence of conserved plant responses to AM symbiosis in a woody perennial species. Among the 18 proteins whose amount was reduced in AMF-colonised roots were proteins involved in glycolysis, protein synthesis and fate, defence and cell rescue, ethylene biosynthesis and purine and pyrimidine salvage degradation. The six co-identified proteins whose amount was increased had functions in energy production, signalling, protein synthesis and fate including proteases. Altogether these data confirmed that a part of the accommodation program of AMF previously characterized in annual plants is maintained within roots of the SO4 rootstock cuttings. Nonetheless, particular responses also occurred involving proteins of carbon metabolism, development and root architecture, defence and cell rescue, anthocyanin biosynthesis and P remobilization, previously reported as induced upon P-starvation. This suggests the occurrence of P reprioritization upon AMF colonization in a woody perennial plant species with agronomical interest.

Root morphological and proteomic responses to growth restriction in maize plants supplied with sufficient N

The primary objective of this study was to better understand how root morphological alteration stimulates N uptake in maize plants after root growth restriction, by investigating the changes in length and number of lateral roots, (15)NO(3)(-) influx, the expression level of the low-affinity Nitrate transporter ZmNrt1.1, and proteomic composition of primary roots. Maize seedlings were hydroponically cultured with three different types of root systems: an intact root system, embryonic roots only, or primary roots only. In spite of sufficient N supply, root growth restriction stimulated compensatory growth of remaining roots, as indicated by the increased lateral root number and root density. On the other hand, there was no significant difference in (15)NO(3)(-) influx between control and primary root plants; neither in ZmNrt1.1 expression levels in primary roots of different treatments. Our data suggested that increased N uptake by maize seedlings experiencing root growth restriction is attributed to root morphological adaptation, rather than explained by the variation in N uptake activity. Eight proteins were differentially accumulated in embryonic and primary root plants compared to control plants. These differentially accumulated proteins were closely related to signal transduction and increased root growth.

Comparative proteome analysis of metabolic changes by low phosphorus stress in two Brassica napus genotypes

In an attempt to determine the adaptation strategy to phosphorous (Pi) deficiency in oilseed rape, comparative proteome analyses were conducted to investigate the differences of metabolic changes in two oilseed rape genotypes with different tolerance to low phosphorus (LP). Generally in either roots or leaves, there existed few low phosphorus (LP)-induced proteins shared in the two lines. The LP-tolerant genotype 102 maintained higher Pi concentrations than LP-sensitive genotype 105 when growing hydroponically under the 5-μM phosphorus condition. In 102 we observed the downregulation of the proteins related to gene transcription, protein translation, carbon metabolism, and energy transfer in leaves and roots, and the downregulation of proteins related to leaf growth and root cellular organization. But the proteins related to the formation of lateral root were upregulated, such as the auxin-responsive family proteins in roots and the sucrose-phosphate synthase-like protein in roots and leaves. On the other hand, the LP-sensitive genotype 105 maintained the low level of Pi concentrations and suffered high oxidative pressure under the LP condition, and stress-shocking proteins were pronouncedly upregulated such as the proteins for signal transduction, gene transcription, secondary metabolism, universal stress family proteins, as well as the proteins involved in lipid oxygenation and the disease resistance in both leaves and roots. Although the leaf proteins for growth in 105 were downregulated, the protein expressions in roots related to glycolysis and tricarboxylic acid (TCA) cycle were enhanced to satisfy the requirement of organic acid secretion.

Signaling network in sensing phosphate availability in plants

Plants acquire phosphorus in the form of phosphate (Pi), the concentration of which is often limited for plant uptake. Plants have developed diverse responses to conserve and remobilize internal Pi and to enhance Pi acquisition to secure them against Pi deficiency. These responses are achieved by the coordination of an elaborate signaling network comprising local and systemic machineries. Recent advances have revealed several important components involved in this network. Pi functions as a signal to report its own availability. miR399 and sugars act as systemic signals to regulate responses occurring in roots. Hormones also play crucial roles in modulating gene expression and in altering root system architecture. Transcription factors function as a hub to perceive the signals and to elicit steady outputs. In this review, we outline the current knowledge on this subject and present hypotheses pertaining to other potential signals and to the organization and coordination of signaling.

Biochemical and molecular characterization of AtPAP12 and AtPAP26: the predominant purple acid phosphatase isozymes secreted by phosphate-starved Arabidopsis thaliana

Plant purple acid phosphatases (PAPs) belong to a large multigene family whose specific functions in Pi metabolism are poorly understood. Two PAP isozymes secreted by Pi-deficient (-Pi) Arabidopsis thaliana were purified from culture filtrates of -Pi suspension cells. They correspond to an AtPAP12 (At2g27190) homodimer and AtPAP26 (At5g34850) monomer composed of glycosylated 60 and 55 kDa subunit(s), respectively. Each PAP exhibited broad pH activity profiles centred at pH 5.6, and overlapping substrate specificities. Concanavalin-A chromatography resolved a pair of secreted AtPAP26 glycoforms. AtPAP26 is dual targeted during Pi stress because it is also the principal intracellular (vacuolar) PAP up-regulated by -Pi Arabidopsis. Differential glycosylation appears to influence the subcellular targeting and substrate selectivity of AtPAP26. The significant increase in secreted acid phosphatase activity of -Pi seedlings was correlated with the appearance of immunoreactive AtPAP12 and AtPAP26 polypeptides. Analysis of atpap12 and atpap26 T-DNA mutants verified that AtPAP12 and AtPAP26 account for most of the secreted acid phosphatase activity of -Pi wild-type seedlings. Semi-quantitative RT-PCR confirmed that transcriptional controls exert little influence on the up-regulation of AtPAP26 during Pi stress, whereas AtPAP12 transcripts correlate well with relative levels of secreted AtPAP12 polypeptides. We hypothesize that AtPAP12 and AtPAP26 facilitate Pi scavenging from soil-localized organophosphates during nutritional Pi deprivation.

The dual-targeted purple acid phosphatase isozyme AtPAP26 is essential for efficient acclimation of Arabidopsis to nutritional phosphate deprivation

Induction of intracellular and secreted acid phosphatases (APases) is a widespread response of orthophosphate (Pi)-starved (-Pi) plants. APases catalyze Pi hydrolysis from a broad range of phosphomonoesters at an acidic pH. The largest class of nonspecific plant APases is comprised of the purple APases (PAPs). Although the biochemical properties, subcellular location, and expression of several plant PAPs have been described, their physiological functions have not been fully resolved. Recent biochemical studies indicated that AtPAP26, one of 29 PAPs encoded by the Arabidopsis (Arabidopsis thaliana) genome, is the predominant intracellular APase, as well as a major secreted APase isozyme up-regulated by -Pi Arabidopsis. An atpap26 T-DNA insertion mutant lacking AtPAP26 transcripts and 55-kD immunoreactive AtPAP26 polypeptides exhibited: (1) 9- and 5-fold lower shoot and root APase activity, respectively, which did not change in response to Pi starvation, (2) a 40% decrease in secreted APase activity during Pi deprivation, (3) 35% and 50% reductions in free and total Pi concentration, respectively, as well as 5-fold higher anthocyanin levels in shoots of soil-grown -Pi plants, and (4) impaired shoot and root development when subjected to Pi deficiency. By contrast, no deleterious influence of AtPAP26 loss of function occurred under Pi-replete conditions, or during nitrogen or potassium-limited growth, or oxidative stress. Transient expression of AtPAP26-mCherry in Arabidopsis suspension cells verified that AtPAP26 is targeted to the cell vacuole. Our results confirm that AtPAP26 is a principal contributor to Pi stress-inducible APase activity, and that it plays an important role in the Pi metabolism of -Pi Arabidopsis.

Regulation of phosphate starvation responses in plants: signaling players and cross-talks

Phosphate (Pi) availability is a major factor limiting growth, development, and productivity of plants. In both ecological and agricultural contexts, plants often grow in soils with low soluble phosphate content. Plants respond to this situation by a series of developmental and metabolic adaptations that are aimed at increasing the acquisition of this vital nutrient from the soil, as well as to sustain plant growth and survival. The development of a comprehensive understanding of how plants sense phosphate deficiency and coordinate the responses via signaling pathways has become of major interest, and a number of signaling players and networks have begun to surface for the regulation of the phosphate-deficiency response. In practice, application of such knowledge to improve plant Pi nutrition is hindered by complex cross-talks, which are emerging in the face of new data, such as the coordination of the phosphate-deficiency signaling networks with those involved with hormones, photo-assimilates (sugar), as well as with the homeostasis of other ions, such as iron. In this review, we focus on these cross-talks and on recent progress in discovering new signaling players involved in the Pi-starvation responses, such as proteins having SPX domains.