scholarly journals An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Root Growth Regulation Mechanisms in Response to Nitrogen Availability

2019 ◽  
Vol 20 (23) ◽  
pp. 5893 ◽  
Author(s):  
Wei Xin ◽  
Lina Zhang ◽  
Wenzhong Zhang ◽  
Jiping Gao ◽  
Jun Yi ◽  
...  
Keyword(s):  
Root Growth ◽  
Differentially Expressed Genes ◽  
Nitrogen Availability ◽  
Rice Root ◽  
Integrated Analysis ◽  
High Nitrogen ◽  
Rice Roots ◽  
Regulation Mechanisms ◽  
Low Nitrogen ◽  
Nitrogen Conditions

Nitrogen is an essential nutrient for plant growth and basic metabolic processes. Root systems play an important role in the ability of plants to obtain nutrients from the soil, and are closely related to the growth and development of above-ground plants. Root morphology analysis showed that root growth was induced under low-nitrogen conditions and inhibited under high-nitrogen conditions. To better understand the molecular mechanisms and metabolic basis underlying the rice root response to nitrogen availability, an integrated analysis of the rice root transcriptome and metabolome under three environmental conditions (low-, control, and high-nitrogen conditions) was conducted. A total of 262 and 262 differentially level metabolites were identified under low- and high-nitrogen conditions, respectively. A total of 696 and 808 differentially expressed genes were identified under low- and high-nitrogen conditions, respectively. For both the differentially expressed genes and metabolites, KEGG pathway analysis indicated that amino acid metabolism, carbon and nitrogen metabolism, phenylpropanoid metabolism, and phytohormones’ signal transduction were significantly affected by nitrogen availability. Additionally, variable levels of 65 transcription factors (TFs) were identified in rice leaves exposed to high and low nitrogen, covering 22 TF families. These results also indicate that there is a significant difference in the transcriptional regulation mechanisms of rice roots between low and high nitrogen. In summary, our study provides new information for a further understanding of the response of rice roots to low-nitrogen and high-nitrogen conditions.

scholarly journals Adaptation Mechanism of Roots to Low and High Nitrogen Revealed by Proteomic Analysis

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Wei Xin ◽  
Lina Zhang ◽  
Jiping Gao ◽  
Wenzhong Zhang ◽  
Jun Yi ◽  
...  
Keyword(s):  
Root Growth ◽  
Nitrogen Use Efficiency ◽  
Root Morphology ◽  
Nitrogen Availability ◽  
Rice Root ◽  
Global Changes ◽  
High Nitrogen ◽  
Nitrogen Use ◽  
Rice Roots ◽  
Use Efficiency

Abstract Background Nitrogen-based nutrients are the main factors affecting rice growth and development. Root systems play an important role in helping plants to obtain nutrients from the soil. Root morphology and physiology are often closely related to above-ground plant organs performance. Therefore, it is important to understand the regulatory effects of nitrogen (N) on rice root growth to improve nitrogen use efficiency. Results In this study, changes in the rice root traits under low N (13.33 ppm), normal N (40 ppm) and high N (120 ppm) conditions were performed through root morphology analysis. These results show that, compared with normal N conditions, root growth is promoted under low N conditions, and inhibited under high N conditions. To understand the molecular mechanism underlying the rice root response to low and high N conditions, comparative proteomics analysis was performed using a tandem mass tag (TMT)-based approach, and differentially abundant proteins (DAPs) were further characterized. Compared with normal N conditions, a total of 291 and 211 DAPs were identified under low and high N conditions, respectively. The abundance of proteins involved in cell differentiation, cell wall modification, phenylpropanoid biosynthesis, and protein synthesis was differentially altered, which was an important reason for changes in root morphology. Furthermore, although both low and high N can cause nitrogen stress, rice roots revealed obvious differences in adaptation to low and high N. Conclusions These results provide insights into global changes in the response of rice roots to nitrogen availability and may facilitate the development of rice cultivars with high nitrogen use efficiency through root-based genetic improvements.

scholarly journals Relationship of Nitrogen Use Efficiency with the Activities of Enzymes Involved in Nitrogen Uptake and Assimilation of Finger Millet Genotypes Grown under Different Nitrogen Inputs

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Nidhi Gupta ◽  
Atul K. Gupta ◽  
Vikram S. Gaur ◽  
Anil Kumar
Keyword(s):  
Nitrogen Uptake ◽  
Nitrogen Use Efficiency ◽  
Finger Millet ◽  
High Nitrogen ◽  
Nitrogen Use ◽  
Nitrogen Uptake Efficiency ◽  
Yield Parameters ◽  
Use Efficiency ◽  
Low Nitrogen ◽  
Nitrogen Conditions

Nitrogen responsiveness of three-finger millet genotypes (differing in their seed coat colour) PRM-1 (brown), PRM-701 (golden), and PRM-801 (white) grown under different nitrogen doses was determined by analyzing the growth, yield parameters and activities of nitrate reductase (NR), glutamine synthetase (GS), glutamate synthase; GOGAT, and glutamate dehydrogenase (GDH) at different developmental stages. High nitrogen use efficiency and nitrogen utilization efficiency were observed in PRM-1 genotype, whereas high nitrogen uptake efficiency was observed in PRM-801 genotype. At grain filling nitrogen uptake efficiency in PRM-1 negatively correlated with NR, GS, GOGAT activities whereas it was positively correlated in PRM-701 and PRM-801, however, GDH showed a negative correlation. Growth and yield parameters indicated that PRM-1 responds well at high nitrogen conditions while PRM-701 and PRM-801 respond well at normal and low nitrogen conditions respectively. The study indicates that PRM-1 is high nitrogen responsive and has high nitrogen use efficiency, whereas golden PRM-701 and white PRM-801 are low nitrogen responsive genotypes and have low nitrogen use efficiency. However, the crude grain protein content was higher in PRM-801 genotype followed by PRM-701 and PRM-1, indicating negative correlation of nitrogen use efficiency with source to sink relationship in terms of seed protein content.

scholarly journals MET17 and Hydrogen Sulfide Formation inSaccharomyces cerevisiae

2000 ◽  
Vol 66 (10) ◽  
pp. 4421-4426 ◽  
Author(s):  
Apostolos Spiropoulos ◽  
Linda F. Bisson
Keyword(s):  
Hydrogen Sulfide ◽  
Fold Increase ◽  
High Nitrogen ◽  
Level Of Activity ◽  
Production Of Hydrogen ◽  
Reduced Sulfur ◽  
The Impact ◽  
Low Nitrogen ◽  
Production Conditions ◽  
Nitrogen Conditions

ABSTRACT Commercial isolates of Saccharomyces cerevisiae differ in the production of hydrogen sulfide (H2S) during fermentation, which has been attributed to variation in the ability to incorporate reduced sulfur into organic compounds. We transformed two commercial strains (UCD522 and UCD713) with a plasmid overexpressing the MET17 gene, which encodes the bifunctionalO-acetylserine/O-acetylhomoserine sulfhydrylase (OAS/OAH SHLase), to test the hypothesis that the level of activity of this enzyme limits reduced sulfur incorporation, leading to H2S release. Overexpression of MET17 resulted in a 10- to 70-fold increase in OAS/OAH SHLase activity in UCD522 but had no impact on the level of H2S produced. In contrast, OAS/OAH SHLase activity was not as highly expressed in transformants of UCD713 (0.5- to 10-fold) but resulted in greatly reduced H2S formation. Overexpression of OAS/OAH SHLase activity was greater in UCD713 when grown under low-nitrogen conditions, but the impact on reduction of H2S was greater under high-nitrogen conditions. Thus, there was not a good correlation between the level of enzyme activity and H2S production. We measured cellular levels of cysteine to determine the impact of overexpression of OAS/OAH SHLase activity on sulfur incorporation. While Met17p activity was not correlated with increased cysteine production, conditions that led to elevated cytoplasmic levels of cysteine also reduced H2S formation. Our data do not support the simple hypothesis that variation in OAS/OAH SHLase activity is correlated with H2S production and release.

Photoinactivation and recovery of photosystem II in Chenopodium album leaves grown at different levels of irradiance and nitrogen availability

2002 ◽  
Vol 29 (7) ◽  
pp. 787 ◽  
Author(s):  
Masaharu C. Kato ◽  
Kouki Hikosaka ◽  
Tadaki Hirose
Keyword(s):  
Photosystem Ii ◽  
Protein Turnover ◽  
Nitrogen Availability ◽  
Photosynthetic Capacity ◽  
Chenopodium Album ◽  
D1 Protein ◽  
High Light ◽  
High Nitrogen ◽  
Low Light ◽  
Low Nitrogen

Involvement of photosynthetic capacity and D1 protein turnover in the susceptibility of photosystem II (PSII) to photoinhibition was investigated in leaves of Chenopodium album L. grown at different combinations of irradiance and nitrogen availability: low light and high nitrogen (LL-HN); high light and low nitrogen (HL-LN); and high light and high nitrogen (HL-HN). To test the importance of photosynthetic capacity in the susceptibility to photoinhibition, we adjusted growth conditions so that HL-HN plants had the highest photosynthetic capacity, while that of LL-HN and HL-LN plants was lower but similar to each other. Photoinhibition refers here to net inactivation of PSII determined by the balance between gross inactivation (photoinactivation) and concurrent recovery of PSII via D1 protein turnover. Leaves were illuminated both in the presence and absence of lincomycin, an inhibitor of chloroplast-encoded protein synthesis. Susceptibility to photoinhibition was much higher in plants grown in low light (LL-HN) than those grown in high light (HL-HN and HL-LN). Susceptibility to photoinhibition was similar in HL-LN and HL-HN plants, suggesting that higher photosynthetic energy consumption alone did not mitigate photoinhibition. Experiments with and without lincomycin showed that high-light-grown plants had a lower rate of photoinactivation and a higher rate of concurrent recovery, and that these rates were not influenced by nitrogen availability. These results indicate that turnover of D1 protein plays a crucial role in photoprotection in high-light-grown plants, irrespective of nitrogen availability. For low-nitrogen-grown plants, higher light energy dissipation by other mechanisms may have compensated for lower energy utilization by photosynthesis.

scholarly journals An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Differential Regulation of Carbon and Nitrogen Metabolism in Response to Nitrogen Availability

2019 ◽  
Vol 20 (9) ◽  
pp. 2349 ◽  
Author(s):  
Wei Xin ◽  
Lina Zhang ◽  
Wenzhong Zhang ◽  
Jiping Gao ◽  
Jun Yi ◽  
...  
Keyword(s):  
Nitrogen Metabolism ◽  
Nitrogen Use Efficiency ◽  
Nitrogen Availability ◽  
Tca Cycle ◽  
Integrated Analysis ◽  
Nitrogen Use ◽  
Carbon And Nitrogen ◽  
Use Efficiency ◽  
Carbon And Nitrogen Metabolism ◽  
Low Nitrogen

Nitrogen (N) is an extremely important macronutrient for plant growth and development. It is the main limiting factor in most agricultural production. However, it is well known that the nitrogen use efficiency (NUE) of rice gradually decreases with the increase of the nitrogen application rate. In order to clarify the underlying metabolic and molecular mechanisms of this phenomenon, we performed an integrated analysis of the rice transcriptome and metabolome. Both differentially expressed genes (DEGs) and metabolite Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that carbon and nitrogen metabolism is significantly affected by nitrogen availability. Further analysis of carbon and nitrogen metabolism changes in rice under different nitrogen availability showed that high N inhibits nitrogen assimilation and aromatic metabolism pathways by regulating carbon metabolism pathways such as the tricarboxylic acid (TCA) cycle and the pentose phosphate pathway (PPP). Under low nitrogen, the TCA cycle is promoted to produce more energy and α-ketoglutarate, thereby enhancing nitrogen transport and assimilation. PPP is also inhibited by low N, which may be consistent with the lower NADPH demand under low nitrogen. Additionally, we performed a co-expression network analysis of genes and metabolites related to carbon and nitrogen metabolism. In total, 15 genes were identified as hub genes. In summary, this study reveals the influence of nitrogen levels on the regulation mechanisms for carbon and nitrogen metabolism in rice and provides new insights into coordinating carbon and nitrogen metabolism and improving nitrogen use efficiency in rice.

Research on the Construction and Visualization of a Three-Dimensional Model of Rice Root Growth

2020 ◽  
Vol 36 (6) ◽  
pp. 847-857
Author(s):  
Le   Yang ◽  
Panpan   Wu ◽  
Suyong   Yang ◽  
Peng   Shao
Keyword(s):  
Root Growth ◽  
Growth Model ◽  
Three Dimensional ◽  
Morphological Characteristics ◽  
Rice Root ◽  
Model Output ◽  
Rice Roots ◽  
L System ◽  
Growth Laws ◽  
Dynamic Growth

HighlightsThis article proposes a three-dimensional rice root growth model based on the differential L-system.We tested the accuracy of the model output, and the measured values and the simulated values were compared.A three-dimensional visualization of the growth simulation system was implemented, and the dynamic growth process of rice roots was visually reproduced.Abstract. Three-dimensional visualization studies on the morphological characteristics of rice root systems are important for improving farmland management and for the selective breeding and genetic improvement of rice. To clarify the rules governing the structure and distribution of rice roots, the three-dimensional (3D) coordinates and morphological parameters of rice roots were measured in hydroponic experiments at different growing periods, and the rice root structure was measured with a high degree of accuracy. The initial position, growth direction, and rate were then determined via statistical analysis of the data. In this article, a 3D rice root growth model based on the differential L-system is proposed; in this system, the biological characteristics based on the topological structure and the actual growth laws of rice roots are quantified. We adopted the growing degree day (GDD) as the driving factor that describes the growth law of rice roots and tested the accuracy of the model output. In this model, a 3D visualization of the growth simulation system of rice roots is implemented via Visual C++ and the OpenGL standard library on the basis of algorithms for the constructed 3D rice root growth model. The model output realistically recreates the dynamic growth process of rice roots under different conditions. A large amount of experimental data and comparative analysis show that the average accuracies achieved by the proposed system concerning total root length, root surface area and root volume are 96.95%, 95.97%, and 93.98%, respectively. These results verify the high reliability of the constructed model and the effective simulation of the morphological characteristics and growth laws of rice roots at different growth periods, laying the foundation for future research on the laws of changes in morphological structure and the physiological and ecological factors of rice roots at different growth stages. Keywords: Differential L-system, Rice roots, Simulation, Three-dimensional growth model, Visualization.

Altered weed reproduction and maternal effects under low-nitrogen fertility

Weed Science ◽  
2006 ◽  
Vol 54 (5) ◽  
pp. 847-853 ◽  
Author(s):  
Kimberly D. Tungate ◽  
Michael G. Burton ◽  
David J. Susko ◽  
Shannon M. Sermons ◽  
Thomas W. Rufty
Keyword(s):  
Maternal Effects ◽  
Nitrogen Availability ◽  
Seed Mass ◽  
Weed Suppression ◽  
Low Fertility ◽  
Sand Culture ◽  
Shoot Biomass ◽  
High Nitrogen ◽  
Nitrogen Fertility ◽  
Low Nitrogen

The low-nitrogen status of highly weathered soils may offer a potential alternative for weed suppression in agricultural systems with N2-fixing crops. In this study, we used sicklepod as a model to evaluate weed response that might occur with managed reductions in nitrogen-soil fertility. A field study was conducted with the parental generation supplied 0, 112, 224, or 448 kg N ha−1. Decreased nitrogen fertility led to reduced shoot biomass, seed number, and total seed mass. Individual seed mass was lower, but seed % nitrogen was not affected. Analysis of seed-mass distribution confirmed that low parental fertility was associated with more small seeds as a proportion of total seeds produced. Additional experiments in hydroponics culture revealed slower growth rates of seedlings produced from small seeds when grown under low-nitrogen conditions. Competitiveness of plants from small (low nitrogen) and large (high nitrogen) seed classes was determined in a replacement-series experiment conducted in sand culture in a controlled environment at two densities and two levels of nitrogen nutrition. Plants produced from smaller seeds were less competitive in low-nitrogen fertility conditions, but plants from small and large seeds competed similarly when grown under high-nitrogen fertility. The results support the hypothesis that comprehensive management strategies to reduce nitrogen availability for weed growth in low-fertility conditions could decrease weed interference by decreasing growth and seed production of parental plants and through maternal effects that lower competitiveness of offspring.

Effects of endophyte infection on the competitive ability of Achnatherum sibiricum depend on endophyte species and nitrogen availability

2019 ◽  
Vol 12 (5) ◽  
pp. 815-824
Author(s):  
Yong Zhou ◽  
Xia Li ◽  
Hui Liu ◽  
Yubao Gao ◽  
Wade J Mace ◽  
...  
Keyword(s):  
Dominant Species ◽  
Competitive Ability ◽  
Nitrogen Availability ◽  
Inhibitory Effect ◽  
Nitrogen Supply ◽  
Tiller Number ◽  
High Nitrogen ◽  
Nitrogen Levels ◽  
Endophyte Infection ◽  
Low Nitrogen

Abstract Aims The leaves of almost all terrestrial plant species are colonized by endophytic fungi. Compared to agronomic grasses, which usually harbor few endophytes, native grasses generally possess greater endophyte species diversity. Existing studies examining endophyte effects on natural grasses under competition normally considered the infection status (infected or uninfected), and rarely considered endophyte species. Methods We examined the effects of endophyte infection and of endophyte species on the interspecific competitive ability of a subdominant species, Achnatherum sibiricum, at two nitrogen levels (high nitrogen and low nitrogen). Achnatherum sibiricum plants infected by two different species of endophyte (Epichloë sibirica and E. gansuensis) and uninfected plants were grown in monoculture and binary mixtures with a dominant species, Stipa grandis (six individuals per species for monocultures and three + three individuals of each species in mixtures). Shoot and root biomass, tiller number and total phenolic concentration were measured after 3 months. Moreover, the aggressivity index was calculated to compare the competitive ability of A. sibiricum relative to S. grandis. Important Findings Both E. gansuensis (Eg)- and E. sibirica (Es)-infected A. sibiricum plants showed a greater competitive ability than the uninfected plants under high nitrogen supply, while the opposite result occurred under low nitrogen supply. At high nitrogen levels, Eg plants had a higher tiller number and a greater shoot biomass inhibitory effect on S. grandis than Es plants had when growing in mixture, while Es plants showed better root growth performance than Eg and uninfected plants under mixture conditions at all nitrogen levels. A higher concentration of phenolic compounds in Eg plants than in Es plants might contribute to the higher inhibitory effect of Eg plants on competing plants. Our study indicates that the interaction between endophyte infection and nitrogen availability can alter the competitive ability of the host plant A. sibiricum but that these two endophyte species work in different ways, which may influence the coexistence of A. sibiricum with the dominant species.

scholarly journals A comparative study of genomic adaptations to low nitrogen availability in Genlisea aurea

2021 ◽  
Author(s):  
Thibaut Goldsborough
Keyword(s):  
Comparative Study ◽  
Nitrogen Availability ◽  
Trifolium Pratense ◽  
Nitrogen Starvation ◽  
Model Organism ◽  
Carnivorous Plant ◽  
High Nitrogen Content ◽  
High Nitrogen ◽  
Nitrogen Levels ◽  
Low Nitrogen

AbstractGenlisea aurea is a carnivorous plant that grows on nitrogen-poor waterlogged sandstone plateaus and is thought to have evolved carnivory as an adaptation to very low nitrogen levels in its habitat. The carnivorous plant is also unusual for having one of the smallest genomes among flowering plants. Genomic DNA is known to have a high nitrogen content and yet, to the author’s knowledge, no published study has linked nitrogen starvation of G. aurea with genome size reduction. This comparative study of the carnivorous plant G. aurea, the model organism Arabidopsis thaliana (Brassicaceae) and the nitrogen fixing Trifolium pratense (Fabaceae) attempts to investigate whether the genome, transcriptome and proteome of G. aurea showed evidence of adaptations to low nitrogen availability. It was found that although G. aurea’s genome, CDS and non-coding DNA were much lower in nitrogen than the genome of T. pratense and A. thaliana this was solely due to the length of the genome, CDS and non-coding sequences rather than the composition of these sequences.

Sign in / Sign up

Export Citation Format

Share Document