Integrated Proteomics and Metabolomics Analysis of Nitrogen System Regulation on Soybean Plant Nodulation and Nitrogen Fixation

Lyu, Xiaochen; Sun, Chunyan; Zhang, Jin; Wang, Chang; Zhao, Shuhong; Ma, Chao; Li, Sha; Li, Hongyu; Gong, Zhenping; Yan, Chao

doi:10.3390/ijms23052545

Cited by 11 publications

(5 citation statements)

References 54 publications

(66 reference statements)

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“…It has also been found that exogenous plant hormones help plants resist nitrogen stress by improving GS activity [52]. Lyu et al found that exogenous nitrogen regulates starch, sucrose, and amino acid metabolism and other related metabolic pathways and promotes the synthesis of asparagine and NO; these results are consistent with those of our study [53]. Mauceri et al found that under nitrogen-deficient conditions, the levels of L-aspartic acid and L-asparagine in eggplants increased, and those of particle-bound starch synthase (WAXY) and endonuclease decreased.…”

Section: Discussionsupporting

confidence: 93%

“…Phosphoenolpyruvate carboxylase is known to be upregulated under HN conditions, which is consistent with the results of this study, indicating that phosphoenolpyruvate carboxylase is involved in protecting plants against stress under high levels of nitrogen [59]. Multiple studies have found that transcriptional factor subsets composed of bHLH, MYB, WRKY, and AP2/ERF family members are strongly expressed in response to nitrogen disturbances, which is consistent with the results of this study [42,51,53,60]. In conclusion, the response mechanism of quinoa to nitrogen is mainly regulated by the urea cycle and TCA cycle, which provides a reference basis for breeders to select and develop quinoa strains that are tolerant to low-or high-nitrogen stress in the future, and lays a theoretical foundation for improving the nitrogen fertilizer utilization efficiency of quinoa and other plants.…”

Section: Discussionsupporting

confidence: 91%

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Transcriptome and Metabolome Analyses Reveal Mechanisms Underlying the Response of Quinoa Seedlings to Nitrogen Fertilizers

Wang

Huang

et al. 2023

IJMS

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Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous annual amaranth herb that belongs to the family Chenopodiaceae. Quinoa can be cultivated across a wide range of climatic conditions. With regard to its cultivation, nitrogen-based fertilizers have a demonstrable effect on the growth and development of quinoa. How crops respond to the application of nitrogen affects grain quality and yield. Therefore, to explore the regulatory mechanisms that underlie the responses of quinoa seedlings to the application of nitrogen, we selected two varieties (i.e., Dianli-1299 and Dianli-71) of quinoa seedlings and analyzed them using metabolomic and transcriptomic techniques. Specifically, we studied the mechanisms underlying the responses of quinoa seedlings to varying concentrations of nitrogen by analyzing the dynamics of metabolites and genes involved in arginine biosynthesis; carbon fixation; and alanine, aspartate, and glutamate biosynthetic pathways. Overall, we found that differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) of quinoa are affected by the concentration of nitrogen. We detected 1057 metabolites, and 29,012 genes were annotated for the KEGG. We also found that 15 DEMs and 8 DEGs were key determinants of the differences observed in quinoa seedlings under different nitrogen concentrations. These contribute toward a deeper understanding of the metabolic processes of plants under different nitrogen treatments and provide a theoretical basis for improving the nitrogen use efficiency (NUE) of quinoa.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionsupporting

confidence: 91%

Transcriptome and Metabolome Analyses Reveal Mechanisms Underlying the Response of Quinoa Seedlings to Nitrogen Fertilizers

Wang

Huang

et al. 2023

IJMS

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“…Cyanide is an important secondary metabolite acquired during the early fixed period of plant development. Various amino acids, including glutamate, cysteine, glycine, and methionine, are the forerunners in the oxidative decarboxylation processes [ 68 ]. A. niger , isolated from tomato rhizosphere soils, produces HCN and ammonia that adequately enhance the growth of tomato plants [ 69 ].…”

Section: Microbial Communities’ Beneficial Association In the Rhizosp...mentioning

confidence: 99%

Fungi That Promote Plant Growth in the Rhizosphere Boost Crop Growth

Adedayo

Babalola

2023

JoF

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The fungi species dwelling in the rhizosphere of crop plants, revealing functions that endeavor sustainability of the plants, are commonly referred to as ‘plant-growth-promoting fungi’ (PGPF). They are biotic inducers that provide benefits and carry out important functions in agricultural sustainability. The problem encountered in the agricultural system nowadays is how to meet population demand based on crop yield and protection without putting the environment and human and animal health at risk based on crop production. PGPF including Trichoderma spp., Gliocladium virens, Penicillium digitatum, Aspergillus flavus, Actinomucor elegans, Podospora bulbillosa, Arbuscular mycorrhizal fungi, etc., have proven their ecofriendly nature to ameliorate the production of crops by improving the growth of the shoots and roots of crop plants, the germination of seeds, the production of chlorophyll for photosynthesis, and the abundant production of crops. PGPF’s potential mode of action is as follows: the mineralization of the major and minor elements required to support plants’ growth and productivity. In addition, PGPF produce phytohormones, induced resistance, and defense-related enzymes to inhibit or eradicate the invasion of pathogenic microbes, in other words, to help the plants while encountering stress. This review portrays the potential of PGPF as an effective bioagent to facilitate and promote crop production, plant growth, resistance to disease invasion, and various abiotic stresses.

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“…Liquid chromatography-tandem mass spectroscopy (LC-MS/MS) analysis was performed on a Q Exactive mass spectrometer (Thermo Scientific) that was coupled to Easy nLC instrument (Proxeon Biosystems, now Thermo Fisher Scientific) for 60/90 min. The peptides were loaded onto a reversedphase trap column (Thermo Scientific Acclaim PepMap100, 100 µm × 2 cm, nanoViper C 18 ) connected to a C 18 reversedphase analytical Easy Column (10 cm long, 75 µm inner diameter, 3 µm resin; Thermo Scientific) in buffer A (0.1% formic acid) and separated with a linear gradient of buffer B (84% acetonitrile and 0.1% formic acid) at a flow rate of 300 nl/min controlled by IntelliFlow technology, as described by Lyu et al (2022) and Wang et al (2022). After chromatographic separation, the sample was analyzed on a Q Exactive Mass Spectrometer in positive ion mode; the detailed methods used for detection are provided in Supplementary method 2.…”

Section: Tandem Mass Tag Labeling and Protein Digestionmentioning

confidence: 99%

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

et al. 2022

Front. Plant Sci.

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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.

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Integrated Proteomics and Metabolomics Analysis of Nitrogen System Regulation on Soybean Plant Nodulation and Nitrogen Fixation

Cited by 11 publications

References 54 publications

Transcriptome and Metabolome Analyses Reveal Mechanisms Underlying the Response of Quinoa Seedlings to Nitrogen Fertilizers

Transcriptome and Metabolome Analyses Reveal Mechanisms Underlying the Response of Quinoa Seedlings to Nitrogen Fertilizers

Fungi That Promote Plant Growth in the Rhizosphere Boost Crop Growth

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

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