Nitrogen-Deficiency Stress Induces Protein Expression Differentially in Low-N Tolerant and Low-N Sensitive Maize Genotypes

Mining genic resources regulating nitrogen-use efficiency based on integrative biological analyses and their breeding applications in maize and other crops

Nitrogen (N) is an essential factor for limiting crop yields, and cultivation of crops with low nitrogen-use efficiency (NUE) exhibits increasing environmental and ecological risks. Hence, it is crucial to mine valuable NUE improvement genes, which is very important to develop and breed new crop varieties with high NUE in sustainable agriculture system. Quantitative trait locus (QTL) and genome-wide association study (GWAS) analysis are the most common methods for dissecting genetic variations underlying complex traits. In addition, with the advancement of biotechnology, multi-omics technologies can be used to accelerate the process of exploring genetic variations. In this study, we integrate the substantial data of QTLs, quantitative trait nucleotides (QTNs) from GWAS, and multi-omics data including transcriptome, proteome, and metabolome and further analyze their interactions to predict some NUE-related candidate genes. We also provide the genic resources for NUE improvement among maize, rice, wheat, and sorghum by homologous alignment and collinearity analysis. Furthermore, we propose to utilize the knowledge gained from classical cases to provide the frameworks for improving NUE and breeding N-efficient varieties through integrated genomics, systems biology, and modern breeding technologies.

Integrated Transcriptomic and Proteomic Analyses of Low-Nitrogen-Stress Tolerance and Function Analysis of ZmGST42 Gene in Maize

Maize (Zea mays L.) is one of the major staple crops providing human food, animal feed, and raw material support for biofuel production. For its growth and development, maize requires essential macronutrients. In particular, nitrogen (N) plays an important role in determining the final yield and quality of a maize crop. However, the excessive application of N fertilizer is causing serious pollution of land area and water bodies. Therefore, cultivating high-yield and low-N-tolerant maize varieties is crucial for minimizing the nitrate pollution of land and water bodies. Here, based on the analysis of the maize leaf transcriptome and proteome at the grain filling stage, we identified 3957 differentially expressed genes (DEGs) and 329 differentially abundant proteins (DAPs) from the two maize hybrids contrasting in N stress tolerance (low-N-tolerant XY335 and low-N-sensitive HN138) and screened four sets of low-N-responsive genes and proteins through Venn diagram analysis. We identified 761 DEGs (253 up- and 508 down-regulated) specific to XY335, whereas 259 DEGs (198 up- and 61 down-regulated) were specific to HN138, and 59 DEGs (41 up- and 18 down-regulated) were shared between the two cultivars under low-N-stress conditions. Meanwhile, among the low-N-responsive DAPs, thirty were unique to XY335, thirty were specific to HN138, and three DAPs were shared between the two cultivars under low-N treatment. Key among those genes/proteins were leucine-rich repeat protein, DEAD-box ATP-dependent RNA helicase family proteins, copper transport protein, and photosynthesis-related proteins. These genes/proteins were involved in the MAPK signaling pathway, regulating membrane lipid peroxidation, and photosynthesis. Our results may suggest that XY335 better tolerates low-N stress than HN138, possibly through robust low-N-stress sensing and signaling, amplified protein phosphorylation and stress response, and increased photosynthesis efficiency, as well as the down-regulation of 'lavish' or redundant proteins to minimize N demand. Additionally, we screened glutathione transferase 42 (ZmGST42) and performed physiological and biochemical characterizations of the wild-type (B73) and gst42 mutant at the seedling stage. Resultantly, the wild-type exhibited stronger tolerance to low N than the mutant line. Our findings provide a better understanding of the molecular mechanisms underlying low-N tolerance during the maize grain filling stage and reveal key candidate genes for low-N-tolerance breeding in maize.

Current Progress and Future Prospect of Wheat Genetics Research towards an Enhanced Nitrogen Use Efficiency

To improve the yield and quality of wheat is of great importance for food security worldwide. One of the most effective and significant approaches to achieve this goal is to enhance the nitrogen use efficiency (NUE) in wheat. In this review, a comprehensive understanding of the factors involved in the process of the wheat nitrogen uptake, assimilation and remobilization of nitrogen in wheat were introduced. An appropriate definition of NUE is vital prior to its precise evaluation for the following gene identification and breeding process. Apart from grain yield (GY) and grain protein content (GPC), the commonly recognized major indicators of NUE, grain protein deviation (GPD) could also be considered as a potential trait for NUE evaluation. As a complex quantitative trait, NUE is affected by transporter proteins, kinases, transcription factors (TFs) and micro RNAs (miRNAs), which participate in the nitrogen uptake process, as well as key enzymes, circadian regulators, cross-talks between carbon metabolism, which are associated with nitrogen assimilation and remobilization. A series of quantitative genetic loci (QTLs) and linking markers were compiled in the hope to help discover more efficient and useful genetic resources for breeding program. For future NUE improvement, an exploration for other criteria during selection process that incorporates morphological, physiological and biochemical traits is needed. Applying new technologies from phenomics will allow high-throughput NUE phenotyping and accelerate the breeding process. A combination of multi-omics techniques and the previously verified QTLs and molecular markers will facilitate the NUE QTL-mapping and novel gene identification.

Exogenous silicon alleviates the adverse effects of cinnamic acid-induced autotoxicity stress on cucumber seedling growth

Autotoxicity is a key factor that leads to obstacles in continuous cropping systems. Although Si is known to improve plant resistance to biotic and abiotic stresses, little is known about its role in regulating leaf water status, mineral nutrients, nitrogen metabolism, and root morphology of cucumber under autotoxicity stress. Here, we used cucumber seeds (Cucumis sativus L. cv. "Xinchun No. 4") to evaluate how exogenous Si (1 mmol L^-1) affected the leaf water status, mineral nutrient uptake, N metabolism-related enzyme activities, root morphology, and shoot growth of cucumber seedlings under 0.8 mmol L^-1 CA-induced autotoxicity stress. We found that CA-induced autotoxicity significantly reduced the relative water content and water potential of leaves and increase their cell sap concentration. CA-induced stress also inhibited the absorption of major (N, P, K, Ca, Mg) and trace elements (Fe, Mn, Zn). However, exogenous Si significantly improved the leaf water status (relative water content and water potential) of cucumber leaves under CA-induced stress. Exogenous Si also promoted the absorption of mineral elements by seedlings under CA-induced stress and alleviated the CA-induced inhibition of N metabolism-related enzyme activities (including nitrate reductase, nitrite reductase, glutamine synthetase, glutamate synthase, glutamate dehydrogenase). Moreover, exogenous Si improved N uptake and utilization, promoted root morphogenesis, and increased the growth indexes of cucumber seedlings under CA-induced stress. Our findings have far-reaching implications for overcoming the obstacles to continuous cropping in cucumber cultivation.

Identification and expression analysis of GARP superfamily genes in response to nitrogen and phosphorus stress in Spirodela polyrhiza

BACKGROUND

GARP transcription factors perform critical roles in plant development and response to environmental stimulus, especially in the phosphorus (P) and nitrogen (N) sensing and uptake. Spirodela polyrhiza (giant duckweed) is widely used for phytoremediation and biomass production due to its rapid growth and efficient N and P removal capacities. However, there has not yet been a comprehensive analysis of the GRAP gene family in S. polyrhiza.

RESULTS

We conducted a comprehensive study of GRAP superfamily genes in S. polyrhiza. First, we investigated 35 SpGARP genes which have been classified into three groups based on their gene structures, conserved motifs, and phylogenetic relationship. Then, we identified the duplication events, performed the synteny analysis, and calculated the K_a/K_s ratio in these SpGARP genes. The regulatory and co-expression networks of SpGARPs were further constructed using cis-acting element analysis and weighted correlation network analysis (WGCNA). Finally, the expression pattern of SpGARP genes were analyzed using RNA-seq data and qRT-PCR, and several NIGT1 transcription factors were found to be involved in both N and P starvation responses.

CONCLUSIONS

The study provides insight into the evolution and function of GARP superfamily in S. polyrhiza, and lays the foundation for the further functional verification of SpGARP genes.

How does nitrate regulate plant senescence?

Nitrogen is an essential macronutrient for plant growth and development and plays an important role in the whole life process of plants. Nitrogen is an important component of amino acids, chlorophyll, plant hormones and secondary metabolites. Nitrogen deficiency leads to early senescence in plants, which is accompanied by changes in gene expression, metabolism, growth, development, and physiological and biochemical traits, which ensures efficient nitrogen recycling and enhances the plant's tolerance to low nitrogen. Therefore, it is very important to understand the adaptation mechanisms of plants under nitrogen deficiency for the efficient utilization of nitrogen and gene regulation. With the popularization of molecular biology, bioinformatics and transgenic technology, the metabolic pathways of nitrogen-deficient plants have been verified, and important progress has been made. However, how the responses of plants to nitrogen deficiency affect the biological processes of the plants is not well understood. The current research also cannot completely explain how the metabolic pathways identified show other reactions or phenotypes through interactions or cascades after nitrogen inhibition. Nitrate is the main form of nitrogen absorption. In this review, we discuss the role of nitrate in plant senescence. Understanding how nitrate inhibition affects nitrate absorption, transport, and assimilation; chlorophyll synthesis; photosynthesis; anthocyanin synthesis; and plant hormone synthesis is key to sustainable agriculture.

Metabolite Profiling and Network Analysis Reveal Coordinated Changes in Low-N Tolerant and Low-N Sensitive Maize Genotypes under Nitrogen Deficiency and Restoration Conditions

Nitrogen (N), applied in the form of a nitrogenous fertilizer, is one of the main inputs for agricultural production. Food production is closely associated with the application of N. However, the application of nitrogenous fertilizers to agricultural fields is associated with heavy production of nitrous oxide because agricultural crops can only utilize 30-40% of applied N, leaving behind unused 60-70% N in the environment. The global warming effect of this greenhouse gas is approximately 300 times more than of carbon dioxide. Under the present scenario of climate change, it is critical to maintain the natural balance between food production and environmental sustainability by targeting traits responsible for improving nitrogen-use-efficiency (NUE). Understanding of the molecular mechanisms behind the metabolic alterations due to nitrogen status needs to be addressed. Additionally, mineral nutrient deficiencies and their associated metabolic networks have not yet been studied well. Given this, the alterations in core metabolic pathways of low-N tolerant (LNT) and low-N sensitive (LNS) genotypes of maize under N-deficiency and their efficiency of recovering the changes upon resupplying N were investigated by us, using the GC-MS and LC-MS based metabolomic approach. Significant genotype-specific changes were noted in response to low-N. The N limitation affected the whole plant metabolism, most significantly the precursors of primary metabolic pathways. These precursors may act as important targets for improving the NUE. Limited availability of N reduced the levels of N-containing metabolites, organic acids and amino acids, but soluble sugars increased. Major variations were encountered in LNS, as compared to LNT. This study has revealed potential metabolic targets in response to the N status, which are indeed the prospective targets for crop improvement.

Grain Yields and Nitrogen Use Efficiencies in Different Types of Stay-Green Maize in Response to Nitrogen Fertilizer

The stay-green leaf phenotype is typically associated with increased yields and improved stress resistance in maize breeding, due to higher nitrogen (N) nutrient levels that prolong greenness. The application of N fertilizer can regulate the N status of plants, and furthermore, impact the photosynthetic rates of leaves at the productive stage; however, N deficiencies and N excesses will reduce maize yields. Consequently, it is necessary to develop N fertilizer management strategies for different types of stay-green maize. For this study, the senescent cultivar Lianchuang 808 (LC808), moderate-stay-green cultivar Zhengdan 958 (ZD958), and over stay-green cultivar Denghai 685 (DH685) were selected as experimental models. Our results revealed that yields of ZD958 were slightly higher than DH685 and notably improved over than LC808. Compared with a non-stay-green cultivar LC808, ZD958 and DH685 still maintained higher chlorophyll contents and cell activities following the silking stage, while efficiently slowing the senescence rate. The supply of N fertilizer significantly prolonged leaf greenness and delayed senescence for ZD958 and DH685; however, the effect was not obvious for LC808. The stem remobilization efficiency of N was higher in the moderate-stay-green cultivar ZD958, in contrast to LC808, while the transfer of leaf N was lower than LC808, which guaranteed high leaf N levels, and that sufficient N was transferred to grains in ZD958. To obtain the highest yields, the optimal N fertilizer rates were 228.1 kg hm⁻² for LC0808, 180 kg hm⁻² for ZD958, and 203.8 kg hm⁻² for DH685. In future, the selection of stay-green type crops might serve as an important agricultural strategy to reduce the quantity of N fertilizer and increase N efficiency.

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.

Protein Phosphatase (PP2C9) Induces Protein Expression Differentially to Mediate Nitrogen Utilization Efficiency in Rice under Nitrogen-Deficient Condition

Nitrogen (N) is an essential element usually limiting in plant growth and a basic factor for increasing the input cost in agriculture. To ensure the food security and environmental sustainability it is urgently required to manage the N fertilizer. The identification or development of genotypes with high nitrogen utilization efficiency (NUE) which can grow efficiently and sustain yield in low N conditions is a possible solution. In this study, two isogenic rice genotypes i.e., wild-type rice kitaake and its transgenic line PP2C9TL overexpressed protein phosphatase gene (PP2C9) were used for comparative proteomics analysis at control and low level of N to identify specific proteins and encoding genes related to high NUE. 2D gel electrophoresis was used to perform the differential proteome analysis. In the leaf proteome, 30 protein spots were differentially expressed between the two isogenic lines under low N level which were involved in the process of energy, photosynthesis, N metabolism, signaling, and defense mechanisms. In addition, we have found that protein phosphatase enhances nitrate reductase activation by downregulation of SnRK1 and 14-3-3 proteins. Furthermore, we showed that PP2C9TL exhibits higher NUE than WT due to higher activity of nitrate reductase. This study provides new insights on the rice proteome which would be useful in the development of new strategies to increase NUE in cereal crops.

Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants

Long non-coding RNA (lncRNA) research in plants has recently gained momentum taking cues from studies in animals systems. The availability of next-generation sequencing has enabled genome-wide identification of lncRNA in several plant species. Some lncRNAs are inhibitors of microRNA expression and have a function known as target mimicry with the sequestered transcript known as an endogenous target mimic (eTM). The lncRNAs identified to date show diverse mechanisms of gene regulation, most of which remain poorly understood. In this review, we discuss the role of identified putative lncRNAs that may act as eTMs for nutrient-responsive microRNAs (miRNAs) in plants. If functionally validated, these putative lncRNAs would enhance current understanding of the role of lncRNAs in nutrient homeostasis in plants.

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.

Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae

To understand the post-transcriptional molecular mechanisms attributing to oleaginousness in microalgae challenged with nitrogen starvation (N-starvation), the longitudinal proteome dynamics of Chlorella sp. FC2 IITG was investigated using multipronged quantitative proteomics and multiple reaction monitoring assays. Physiological data suggested a remarkably enhanced lipid accumulation with concomitant reduction in carbon flux towards carbohydrate, protein and chlorophyll biosynthesis. The proteomics-based investigations identified the down-regulation of enzymes involved in chlorophyll biosynthesis (porphobilinogen deaminase) and photosynthetic carbon fixation (sedoheptulose-1,7 bisphosphate and phosphoribulokinase). Profound up-regulation of hydroxyacyl-ACP dehydrogenase and enoyl-ACP reductase ascertained lipid accumulation. The carbon skeletons to be integrated into lipid precursors were regenerated by glycolysis, β-oxidation and TCA cycle. The enhanced expression of glycolysis and pentose phosphate pathway enzymes indicates heightened energy needs of FC2 cells for the sustenance of N-starvation. FC2 cells strategically reserved nitrogen by incorporating it into the TCA-cycle intermediates to form amino acids; particularly the enzymes involved in the biosynthesis of glutamate, aspartate and arginine were up-regulated. Regulation of arginine, superoxide dismutase, thioredoxin-peroxiredoxin, lipocalin, serine-hydroxymethyltransferase, cysteine synthase, and octanoyltransferase play a critical role in maintaining cellular homeostasis during N-starvation. These findings may provide a rationale for genetic engineering of microalgae, which may enable synchronized biomass and lipid synthesis.

Revealing new insights into different phosphorus-starving responses between two maize (Zea mays) inbred lines by transcriptomic and proteomic studies

Phosphorus (P) is an essential plant nutrient, and deficiency of P is one of the most important factors restricting maize yield. Therefore, it is necessary to develop a more efficient program of P fertilization and breeding crop varieties with enhanced Pi uptake and use efficiency, which required understanding how plants respond to Pi starvation. To understand how maize plants adapt to P-deficiency stress, we screened 116 inbred lines in the field and identified two lines, DSY2 and DSY79 that were extreme low-P resistant and sensitive, respectively. We further conducted physiological, transcriptomic, and proteomic studies using the roots of DSY2 and DSY79 under normal or low-P conditions. The results showed that the low-P resistant line, DSY2 had larger root length, surface area and volume, higher root vitality, as well as acid phosphatase activity as compared with the low-P sensitive line, DSY79 under the low-P condition. The transcriptomic and proteomic results suggest that dramatic more genes were induced in DSY2, including the plant hormone signaling, acid phosphatase, and metabolite genes, as compared with DSY79 after being challenged by low-P stress. The new insights generated in this study will be useful toward the improvement of P-utilize efficiency in maize.

Comparative Transcriptome Analysis Revealed Genes Commonly Responsive to Varied Nitrate Stress in Leaves of Tibetan Hulless Barley

Nitrogen (N) deprivation or excess can lead to dramatic phenotype change, disrupt important biological processes, and ultimately limit plant productivity. To explore genes in Tibetan hulless barley responsive to varied N stress, we utilized a comparative transcriptomics method to investigate gene expression patterns under three nitrate treatments. The transcriptome of the control (optimal-nitrate, ON) sample was compared with that of free-nitrate (FN), low-nitrate (LN), and high-nitrate (HN) treatment samples, identifying 2428, 1274, and 1861 genes, respectively, that exhibited significant differences in transcript abundance. Among these, 9 genes encoding ribulose bisphosphate carboxylases exhibited up-regulated expression under varied N stress. We further compared FN vs. ON and LN vs. ON to investigate the impact of stress degree on gene expression. With the aggravation of stress, more genes were differentially expressed and thus possibly involved in the response to nitrogen deficiency. Cluster and functional enrichment analysis indicated that the differentially expressed genes (DEGs) in FN were highly enriched in response to stress, defense response, and gene expression regulation. Comprehensive comparison analysis further suggested that Tibetan hulless barley could respond to varied N stress by regulating multiple common biological processes and pathways such as nitrogen metabolism, carbon metabolism, and photosynthesis. A large number of specific DEGs involved in diverse biological processes were also detected, implying differences in the potential regulatory patterns of low- and high-N stress response. Notably, we also identified some NIN-like proteins and other transcription factors significantly modulated by these stresses, suggesting the involvement of these transcription factors in N stress response. To our knowledge, this study is the first investigation of the Tibetan hulless barley transcriptome under N stress. The identified N-stress-related genes may provide resources for genetic improvement and promote N use efficiency.