Nitrogen stress-induced alterations in the leaf proteome of two wheat varieties grown at different nitrogen levels

Revealing the differential protein profiles behind the nitrogen use efficiency in popcorn (Zea mays var. everta)

We investigated the proteomic profiles of two popcorn inbred lines, P2 (N-efficient and N-responsive) and L80 (N-inefficient and nonresponsive to N), under low (10% of N supply) and high (100% of N supply) nitrogen environments, associated with agronomic- and physiological-related traits to NUE. The comparative proteomic analysis allowed the identification of 79 differentially accumulated proteins (DAPs) in the comparison of high/low N for P2 and 96 DAPs in the comparison of high/low N for L80. The NUE and N uptake efficiency (NUpE) presented high means in P2 in comparison to L80 at both N levels, but the NUE, NUpE, and N utilization efficiency (NUtE) rates decreased in P2 under a high N supply. DAPs involved in energy and carbohydrate metabolism suggested that N regulates enzymes of alternative pathways to adapt to energy shortages and that fructose-bisphosphate aldolase may act as one of the key primary nitrate responsive proteins in P2. Proteins related to ascorbate biosynthesis and nitrogen metabolism increased their regulation in P2, and the interaction of l-ascorbate peroxidase and Fd-NiR may play an important role in the NUE trait. Taken together, our results provide new insights into the proteomic changes taking place in contrasting inbred lines, providing useful information on the genetic improvement of NUE in popcorn.

Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants

C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.

Transcriptomic Study for Identification of Major Nitrogen Stress Responsive Genes in Australian Bread Wheat Cultivars

High nitrogen use efficiency (NUE) in bread wheat is pivotal to sustain high productivity. Knowledge about the physiological and transcriptomic changes that regulate NUE, in particular how plants cope with nitrogen (N) stress during flowering and the grain filling period, is crucial in achieving high NUE. Nitrogen response is differentially manifested in different tissues and shows significant genetic variability. A comparative transcriptome study was carried out using RNA-seq analysis to investigate the effect of nitrogen levels on gene expression at 0 days post anthesis (0 DPA) and 10 DPA in second leaf and grain tissues of three Australian wheat (Triticum aestivum) varieties that were known to have varying NUEs. A total of 12,344 differentially expressed genes (DEGs) were identified under nitrogen stress where down-regulated DEGs were predominantly associated with carbohydrate metabolic process, photosynthesis, light-harvesting, and defense response, whereas the up-regulated DEGs were associated with nucleotide metabolism, proteolysis, and transmembrane transport under nitrogen stress. Protein–protein interaction and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis further revealed that highly interacted down-regulated DEGs were involved in light-harvesting and photosynthesis, and up-regulated DEGs were mostly involved in steroid biosynthesis under N stress. The common down-regulated genes across the cultivars included photosystem II 10 kDa polypeptide family proteins, plant protein 1589 of uncharacterized protein function, etc., whereas common up-regulated genes included glutamate carboxypeptidase 2, placenta-specific8 (PLAC8) family protein, and a sulfate transporter. On the other hand, high NUE cultivar Mace responded to nitrogen stress by down-regulation of a stress-related gene annotated as beta-1,3-endoglucanase and pathogenesis-related protein (PR-4, PR-1) and up-regulation of MYB/SANT domain-containing RADIALIS (RAD)-like transcription factors. The medium NUE cultivar Spitfire and low NUE cultivar Volcani demonstrated strong down-regulation of Photosystem II 10 kDa polypeptide family protein and predominant up-regulation of 11S globulin seed storage protein 2 and protein transport protein Sec61 subunit gamma. In grain tissue, most of the DEGs were related to nitrogen metabolism and proteolysis. The DEGs with high abundance in high NUE cultivar can be good candidates to develop nitrogen stress-tolerant variety with improved NUE.

Transcriptome Analysis of High-NUE (T29) and Low-NUE (T13) Genotypes Identified Different Responsive Patterns Involved in Nitrogen Stress in Ramie (Boehmeria nivea (L.) Gaudich)

Nitrogen-use efficiency (NUE) has significant impacts on plant growth and development. NUE in plants differs substantially in physiological resilience to nitrogen stress; however, the molecular mechanisms underlying enhanced resilience of high-NUE plants to nitrogen deficiency remains unclear. We compared transcriptome-wide gene expression between high-NUE and low-NUE ramie (Boehmeria nivea (L.) Gaudich) genotypes under nitrogen (N)-deficient and normal conditions to identify the transcriptomic expression patterns that contribute to ramie resilience to nitrogen deficiency. Two ramie genotypes with contrasting NUE were used in the study, including T29 (NUE = 46.01%) and T13 (NUE = 15.81%). Our results showed that high-NUE genotypes had higher gene expression under the control condition across 94 genes, including frontloaded genes such as GDSL esterase and lipase, gibberellin, UDP-glycosyltransferase, and omega-6 fatty acid desaturase. Seventeen stress-tolerance genes showed lower expression levels and varied little in response to N-deficiency stress in high-NUE genotypes. In contrast, 170 genes were upregulated under N deficiency in high-NUE genotypes but downregulated in low-NUE genotypes compared with the controls. Furthermore, we identified the potential key genes that enable ramie to maintain physiological resilience under N-deficiency stress, and categorized these genes into three groups based on the transcriptome and their expression patterns. The transcriptomic and clustering analysis of these nitrogen-utilization-related genes could provide insight to better understand the mechanism of linking among the three gene classes that enhance resilience in high-NUE ramie genotypes.

Effects of Independent and Combined Water-Deficit and High-Nitrogen Treatments on Flag Leaf Proteomes during Wheat Grain Development

We present the first comprehensive proteome analysis of wheat flag leaves under water-deficit, high-nitrogen (N) fertilization, and combined treatments during grain development in the field. Physiological and agronomic trait analyses showed that leaf relative water content, total chlorophyll content, photosynthetic efficiency, and grain weight and yield were significantly reduced under water-deficit conditions, but dramatically enhanced under high-N fertilization and moderately promoted under the combined treatment. Two-dimensional electrophoresis detected 72 differentially accumulated protein (DAP) spots representing 65 unique proteins, primarily involved in photosynthesis, signal transduction, carbohydrate metabolism, redox homeostasis, stress defense, and energy metabolism. DAPs associated with photosynthesis and protein folding showed significant downregulation and upregulation in response to water-deficit and high-N treatments, respectively. The combined treatment caused a moderate upregulation of DAPs related to photosynthesis and energy and carbohydrate metabolism, suggesting that high-N fertilization can alleviate losses in yield caused by water-deficit conditions by enhancing leaf photosynthesis and grain storage compound synthesis.

Nitrogen Fertilizer Induced Alterations in The Root Proteome of Two Rice Cultivars

Nitrogen (N) is an essential nutrient for plants and a key limiting factor of crop production. However, excessive application of N fertilizers and the low nitrogen use efficiency (NUE) have brought in severe damage to the environment. Therefore, improving NUE is urgent and critical for the reductions of N fertilizer pollution and production cost. In the present study, we investigated the effects of N nutrition on the growth and yield of the two rice (Oryza sativa L.) cultivars, conventional rice Huanghuazhan and indica hybrid rice Quanliangyou 681, which were grown at three levels of N fertilizer (including 135, 180 and 225 kg/hm², labeled as N9, N12, N15, respectively). Then, a proteomic approach was employed in the roots of the two rice cultivars treated with N fertilizer at the level of N15. A total of 6728 proteins were identified, among which 6093 proteins were quantified, and 511 differentially expressed proteins were found in the two rice cultivars after N fertilizer treatment. These differentially expressed proteins were mainly involved in ammonium assimilation, amino acid metabolism, carbohydrate metabolism, lipid metabolism, signal transduction, energy production/regulation, material transport, and stress/defense response. Together, this study provides new insights into the regulatory mechanism of nitrogen fertilization in cereal crops.

Effects of different nitrogen fertilizers on two wheat cultivars: An integrated approach

Investigation of cultivated plant physiology grown under low energy input plays an important role to indicate their fitness to the new environmental conditions. The durum-wheat cultivars Creso and Dylan were tested to evaluate the growth, production, and proteomic and transcriptomic profiles of the crop under different synthetic and organic nitrogen fertilization regimes. In this work, a two-dimensional gel electrophoresis (2-DE) approach combined with liquid chromatography-mass spectrometry (LC-MS) was used to investigate the protein changes induced by the use of different nitrogen sources (hydrolysate of proteins 1 and 2, rhizovit, synthesis, leather) on wheat plants. Proteomic studies were integrated with qPCR analysis of genes related to glutamine synthetase/glutamine-2-oxoglutarate aminotransferase (GS-GOGAT) and tricarboxylic acid (TCA) metabolic pathways because most relevant for nitrogen-dependent plants growth. The proteomic analysis lead to the isolation of 23 spots that were able to distinguish the analyzed samples. These spots yielded the identification of 60 proteins involved in photosynthesis, glycolysis, and nitrogen metabolism. As an example, the quinone oxidoreductase-like protein and probable glutathione S-transferase GSTU proteins were identified in two spots that represents the most statistically significant ones in Dylan samples. Transcript analysis indicated that related genes exhibited different expression trends; the heat map also revealed the different behaviors of the hydrolysates of the proteins 1 and 2 nitrogen sources. The effects of nitrogenous fertilizers at the proteomic and agronomic levels revealed that plants fertilized with synthesis or rhizovit gave the best results concerning yield, whereas rhizovit and protein hydrolysates were most effective for proteins content in the grain (% of dry weight). Therefore, all parameters measured in this study indicated that different kinds of nitrogen fertilization used have a relevant impact on plant growth and production.

2D-DIGE comparative proteomic analysis of developing wheat grains under high-nitrogen fertilization revealed key differentially accumulated proteins that promote storage protein and starch biosyntheses

Nitrogen (N) serves as a macronutrient that is essential to plant growth and development, and significantly influences storage protein and starch biosyntheses and, ultimately, grain yield and quality. In this study, we performed the first comparative proteomic analysis of developing wheat grains under high-N conditions using 2D-DIGE and tandem mass spectrometry. High-N fertilizer application caused significant increases in ear number, ear grain number, and grain yield. 2D-DIGE identified 142 differentially accumulated proteins (DAPs) during grain development in the elite Chinese bread wheat cultivar Zhongmai 175, of which 132 (93%) were identified by MALDI-TOF/TOF-MS, representing 92 unique proteins. These proteins are involved mainly in energy, N and protein metabolism, carbon metabolism, and starch biosynthesis. Subcellular localization prediction and fluorescence confocal microscopic analysis showed that the DAPs identified were localized mainly in the cytosol and chloroplast. Principal component analysis (PCA) revealed a greater proteomic difference among grain developmental periods than between the high-N and control groups. Protein-protein interaction analysis highlighted a complex network centered around enzymes involved in energy, N and protein metabolism, and starch biosynthesis. Six key DAP genes showed expression patterns consistent with their protein accumulation trends during grain development. A putative metabolic pathway was proposed, with synergistic regulatory networks of grain storage protein and starch biosyntheses in response to high-N application.

Proteomic and genomic responses of plants to nutritional stress

Minerals or trace elements in small amount are essential nutrients for every plant, but when the internal concentration exceeds the threshold, these essential elements do create phytotoxicity. Plant responses to elemental stresses are very common due to different anthropogenic activities; however it is a complex phenomenon with individual characteristics for various species. To cope up with the situation, a plant produces a group of strategies both in proteomic and genomic level to overcome it. Controlling the metal stress is known to activate a multigene response resulting in the changes in various proteins, which directly affects almost all biological processes in a living cell. Therefore, proteomic and genomic approaches can be useful for elucidating the molecular responses under metal stress. For this, it is tried to provide the latest knowledge and techniques used in proteomic and genomic study during nutritional stress and is represented here in review form.

Comparative shoot proteome analysis of two potato (Solanum tuberosum L.) genotypes contrasting in nitrogen deficiency responses in vitro

Aiming at a better understanding of the physiological and biochemical background of nitrogen use efficiency, alterations in the shoot proteome under N-deficiency were investigated in two contrasting potato genotypes grown in vitro with 60 and 7.5mM N, respectively. A gel based proteomic approach was applied to identify candidate proteins associated with genotype specific responses to N-deficiency. 21% of the detected proteins differed in abundance between the two genotypes. Between control and N-deficiency conditions 19.5% were differentially accumulated in the sensitive and 15% in the tolerant genotype. 93% of the highly N-deficiency responsive proteins were identified by MALDI TOF/TOF mass spectrometry. The major part was associated with photosynthesis, carbohydrate metabolism, stress response and regulation. Differential accumulation of enzymes involved in the Calvin cycle and glycolysis suggest activation of alternative carbohydrate pathways. In the tolerant genotype, increased abundance under N-deficiency was also found for enzymes involved in chlorophyll synthesis and stability of enzymes, which increase photosynthetic carbon fixation efficiency. Out of a total of 106 differentially abundant proteins, only eight were detected in both genotypes. Our findings suggest that mutually responsive proteins reflect universal stress responses while adaptation to N-deficiency in metabolic pathways is more genotype specific.

SIGNIFICANCE

Nitrogen losses from arable farm land considerably contribute to environmental pollution. In potato, this is a special problem due cultivation on light soils, irrigation and the shallow root system. Therefore, breeding of cultivars with improved nitrogen use efficiency and stable yields under reduced N fertilization is an important issue. Knowledge of genotype dependent adaptation to N-deficiency at the proteome level can help to understand regulation of N efficiency and development of N-efficient cultivars.