Proteome characterization of two contrasting soybean genotypes in response to different phosphorus treatments

Extensive targeted metabolomics analysis reveals the identification of major metabolites, antioxidants, and disease-resistant active pharmaceutical components in Camellia tuberculata (Camellia L.) seeds

Sect. tuberculata plant belongs to the Camellia genus and is named for the "tuberculiform protuberance on the surface of the ovary and fruit". It is a species of great ornamental value and potential medicinal value. However, little has been reported on the metabolites of C. tuberculata seeds. Therefore, this study was conducted to investigate the metabolites of C. tuberculata seeds based on UPLC/ESI-Q TRAP-MS/MS with extensively targeted metabolomics. A total of 1611 metabolites were identified, including 107 alkaloids, 276 amino acids and derivatives, 283 flavonoids, 86 lignans and coumarins, 181 lipids, 68 nucleotides and derivatives, 101 organic acids, 190 phenolic acids, 10 quinones, 4 steroids, 17 tannins, 111 terpenoids, and 177 other metabolites. We compared the different metabolites in seeds between HKH, ZM, ZY, and LY. The 1311 identified different metabolites were classified into three categories. Sixty-three overlapping significant different metabolites were found, of which lignans and coumarins accounted for the largest proportion. The differentially accumulated metabolites were enriched in different metabolic pathways between HKH vs. LY, HKH vs. ZM, HKH vs. ZY, LY vs. ZY, ZM vs. LY and ZM vs. ZY, with the most abundant metabolic pathways being 4, 2, 4, 7, 7 and 5, respectively (p < 0.05). Moreover, among the top 20 metabolites in each subgroup comparison in terms of difference multiplicity 7, 8 and 13. ZM and ZY had the highest phenolic acid content. Ninety-six disease-resistant metabolites and 48 major traditional Chinese medicine agents were identified based on seven diseases. The results of this study will not only lead to a more comprehensive and in-depth understanding of the metabolic properties of C. tuberculata seeds, but also provide a scientific basis for the excavation and further development of its medicinal value.

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.

Multi-omics analysis of the regulatory effects of low-phosphorus stress on phosphorus transport in soybean roots

The regulatory effects of uneven phosphorus supplies on phosphorus transport in soybean roots are still unclear. To further analyze the regulatory effects of low-phosphorus stress on phosphorus transport in soybean roots and the effects of uneven phosphorus application on the physiological mechanism of phosphorus transport in soybean roots, dual-root soybean plants were prepared via grafting, and a sand culture experiment was performed. From the unfolded cotyledon stage to the initial flowering stage, one side of each dual-root soybean system was irrigated with a low-phosphorus-concentration solution (phosphorus-application [P+] side), and the other side was irrigated with a phosphorus-free nutrient solution (phosphorus-free [P-] side); this setup allowed the study of the effects of different phosphorus supply levels on the expression of genes and proteins and the accumulation of metabolites in soybean roots on the P- side to clarify the method through which phosphorus transport is regulated in soybean roots and to provide a theoretical basis for improving the use rate of phosphorus fertilizer. The results revealed that the unilateral supply of low-concentration phosphorus promoted the uptake of phosphorus by soybean roots and the transport of phosphorus from the P+ side to the P- side. Compared with the normal concentration of phosphorus supply and the phosphorus-free supply, the low concentration phosphorus supply affected the regulation of the metabolic pathways involved in starch and sucrose metabolism, glycolysis, fructose, and mannose metabolism, etc., thereby affecting soybean root phosphorus transport. The low-phosphorus stress inhibited fructose synthesis and sucrose synthase synthesis in the soybean roots and the synthesis of hexokinase (HK) and fructose kinase, which catalyzes the conversion of fructose to fructose-6-phosphate. Low-phosphorus stress promoted the synthesis of sucrose invertase and the conversion of sucrose into maltose by the activity of starch synthase (StS) and stimulated the synthesis of UDPG pyrophosphorylase (UGP) and phosphoglucose isomerase (GP1), which is involved in the conversion of UDP-glucose to glucose-6-phosphate. The phosphorus transport pathway of soybean roots was then affected, which promoted phosphorus allocation to UTP and glucose-6-phosphate. Additionally, low-phosphorus stress hastened glycolysis in the soybean roots and inhibited the synthesis of malic acid, thereby promoting the transport of phosphorus in the roots. In addition, low-phosphorus stress inhibited the synthesis of fructose, mannose, and mannose-1-phosphate and the synthesis of other enzymes involved in phosphorus transport as well as invertase, thereby inhibiting the transport and synthesis of several organic phosphorus-containing compounds.

Proteome Analysis of the Soybean Nodule Phosphorus Response Mechanism and Characterization of Stress-Induced Ribosome Structural and Protein Expression Changes

In agroecosystems, a plant-usable form of nitrogen is mainly generated by legume-based biological nitrogen fixation, a process that requires phosphorus (P) as an essential nutrient. To investigate the physiological mechanism whereby phosphorus influences soybean nodule nitrogen fixation, soybean root nodules were exposed to four phosphate levels: 1 mg/L (P stress), 11 mg/L (P stress), 31 mg/L (Normal P), and 61 mg/L (High P) then proteome analysis of nodules was conducted to identify phosphorus-associated proteome changes. We found that phosphorus stress-induced ribosomal protein structural changes were associated with altered key root nodule protein synthesis profiles. Importantly, up-regulated expression of peroxidase was observed as an important phosphorus stress-induced nitrogen fixation-associated adaptation that supported two nodule-associated activities: scavenging of reactive oxygen species (ROS) and cell wall growth. In addition, phosphorus transporter (PT) and purple acid phosphatase (PAPs) were up-regulated that regulated phosphorus transport and utilization to maintain phosphorus balance and nitrogen fixation function in phosphorus-stressed root nodules.

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.

Characterization of Root System Architecture Traits in Diverse Soybean Genotypes Using a Semi-Hydroponic System

Phenotypic variation and correlations among root traits form the basis for selecting and breeding soybean varieties with efficient access to water and nutrients and better adaptation to abiotic stresses. Therefore, it is important to develop a simple and consistent system to study root traits in soybean. In this study, we adopted the semi-hydroponic system to investigate the variability in root morphological traits of 171 soybean genotypes popularized in the Yangtze and Huaihe River regions, eastern China. Highly diverse phenotypes were observed: shoot height (18.7-86.7 cm per plant with a median of 52.3 cm); total root length (208-1663 cm per plant with a median of 885 cm); and root mass (dry weight) (19.4-251 mg per plant with a median of 124 mg). Both total root length and root mass exhibited significant positive correlation with shoot mass (p ≤ 0.05), indicating their relationship with plant growth and adaptation strategies. The nine selected traits contributed to one of the two principal components (eigenvalues > 1), accounting for 78.9% of the total genotypic variation. Agglomerative hierarchical clustering analysis separated the 171 genotypes into five major groups based on these root traits. Three selected genotypes with contrasting root systems were validated in soil-filled rhizoboxes (1.5 m deep) until maturity. Consistent ranking of the genotypes in some important root traits at various growth stages between the two experiments indicates the reliability of the semi-hydroponic system in phenotyping root trait variability at the early growth stage in soybean germplasms.

Morphological, Biochemical, and Proteomic Studies Revealed Impact of Fe and P Crosstalk on Root Development in Phaseolus vulgaris L

Mineral stress is one of the major abiotic stresses faced by crop plants. The present study was undertaken to investigate the impact of mineral stress (iron (Fe) and phosphorus (P)) on various morphological and biochemical responses of the shoot and root tissues and root architecture of common bean (Phaseolus vulgaris L.). This study also leads us to the identification of P stress responsive proteins. The study was conducted under in vitro conditions, in which seeds of Shalimar French Bean-1 (SFB-1) variety were cultured on four different MGRL medium (control (P₁Fe₁), iron deficient (P₁Fe₀), phosphorus deficient (P₀Fe₁), and phosphorus and iron deficient (P₀Fe₀)). Chlorophyll content of leaves, Fe/P content of root tissues, total sugars, proline, length, and weight of shoot and root tissues were assessed and compared within and between the treatments. The analyzed data revealed significant difference between control and other three treatments. Chlorophyll content of shoots was found significantly decreased under mineral stress treatments P₀Fe₁, P₁Fe₀, and P₀Fe₀ than control. Length and weight of shoot and root were also observed significantly decreased under P₀Fe₁, P₁Fe₀, and P₀Fe₀ as compared to control. Total sugar was significantly higher in P₀Fe₁ of roots in comparison to control. Proline content was significantly higher in both tissues of shoots and roots of plants grown under P₁Fe₀, P₀Fe₁, and P₀Fe₀ than control condition. Furthermore, we unexpectedly observed the recovery of roots (mainly primary roots) under P₀Fe₀ as compared to P₁Fe₀ and P₀Fe₁^. Interestingly higher concentration of Fe was also observed in P₀Fe₁ compared to other treatments and also higher concentration of P was observed in P₁Fe₁. These findings suggested that there is a crosstalk between Fe and P and also revealed that there is a disruption in the ability of PR (primary root) to sense local P deficiency in the absence of Fe. Furthermore, proteomics analysis (SDS-PAGE followed by MALDI MS) helped in identification of defensive proteins in P stress condition compared to control.