iTRAQ-based quantitative proteomic and physiological analysis of the response to N deficiency and the compensation effect in rice

Root physiological and soil microbial mechanisms underlying responses to nitrogen deficiency and compensation in Indica and Japonica rice

Compensatory effects are common biological phenomena in nature. In this study, we investigated the changes in root nitrogen uptake, root morphological and physiological responses, and changes in the rhizosphere soil microbial communities of indica and japonica rice during a nitrogen deficiency-sensitive period and an effective compensation period with double the nitrogen supply. We conducted a bucket experiment using Suxiu 867 (a japonica rice variety) and Yangxian You 918 (an indica rice variety). Treatments included CK (constant distribution of nitrogen fertilizer at each growth stage, represented by CK867 and CK918) and NDC (nitrogen deficiency in the tillering stage, double nitrogen application in the ear differentiation stage to compensate, represented by NDC867 and NDC918) variations. Both varieties presented the highest δ15N and 15N abundances and Ndff (refers to the proportion of nitrogen in a plant's body that comes directly from the fertilizer applied.) in rice under the NDC treatment. Metagenomic sequencing of rhizospheric soil showed that the dominant bacterial groups at the phylum level among each treatment were Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, Gemmatimonadetes, and Nitrospirae. The rhizosphere of indica rice was more enriched with the microbial communities involved in nitrogen metabolism, which contributed to higher nitrogen utilization efficiency. A correlation-based network was constructed and provides insights into the formation of nitrogen deficiency compensation effects and contributes to the enhancement of nitrogen uptake and utilization efficiency in rice production.

Integrated Review of Transcriptomic and Proteomic Studies to Understand Molecular Mechanisms of Rice's Response to Environmental Stresses

Rice (Oryza sativa L.) is grown nearly worldwide and is a staple food for more than half of the world's population. With the rise in extreme weather and climate events, there is an urgent need to decode the complex mechanisms of rice's response to environmental stress and to breed high-yield, high-quality and stress-resistant varieties. Over the past few decades, significant advancements in molecular biology have led to the widespread use of several omics methodologies to study all aspects of plant growth, development and environmental adaptation. Transcriptomics and proteomics have become the most popular techniques used to investigate plants' stress-responsive mechanisms despite the complexity of the underlying molecular landscapes. This review offers a comprehensive and current summary of how transcriptomics and proteomics together reveal the molecular details of rice's response to environmental stresses. It also provides a catalog of the current applications of omics in comprehending this imperative crop in relation to stress tolerance improvement and breeding. The evaluation of recent advances in CRISPR/Cas-based genome editing and the application of synthetic biology technologies highlights the possibility of expediting the development of rice cultivars that are resistant to stress and suited to various agroecological environments.

OsG6PGH1 affects various grain quality traits and participates in the salt stress response of rice

Cytoplasmic 6-phosphogluconate dehydrogenase (G6PGH) is a key enzyme in the pentose phosphate pathway that is involved in regulating various biological processes such as material metabolism, and growth and development in plants. However, it was unclear if OsG6PGH1 affected rice grain quality traits. We perform yeast one-hybrid experiments and reveal that OsG6PGH1 may interact with OsAAP6. Subsequently, yeast in vivo point-to-point experiments and local surface plasmon resonance experiments verified that OsG6PGH1 can bind to OsAAP6. OsG6PGH1 in rice is a constitutive expressed gene that may be localized in the cytoplasm. OsAAP6 and protein-synthesis metabolism-related genes are significantly upregulated in OsG6PGH1 overexpressing transgenic positive endosperm, corresponding to a significant increase in the number of protein bodies II, promoting accumulation of related storage proteins, a significant increase in grain protein content (GPC), and improved rice nutritional quality. OsG6PGH1 positively regulates amylose content, negatively regulates chalkiness rate and taste value, significantly affects grain quality traits such as appearance, cooking, and eating qualities of rice, and is involved in regulating the expression of salt stress related genes, thereby enhancing the salt-stress tolerance of rice. Therefore, OsG6PGH1 represents an important genetic resource to assist in the design of high-quality and multi-resistant rice varieties.

Integrated 16S and metabolomics revealed the mechanism of drought resistance and nitrogen uptake in rice at the heading stage under different nitrogen levels

The normal methods of agricultural production worldwide have been strongly affected by the frequent occurrence of drought. Rice rhizosphere microorganisms have been significantly affected by drought stress. To provide a hypothetical basis for improving the drought resistance and N utilization efficiency of rice, the study adopted a barrel planting method at the heading stage, treating rice with no drought or drought stress and three different nitrogen (N) levels. Untargeted metabolomics and 16S rRNA gene sequencing technology were used to study the changes in microorganisms in roots and the differential metabolites (DMs) in rhizosphere soil. The results showed that under the same N application rate, the dry matter mass, N content and N accumulation in rice plants increased to different degrees under drought stress. The root soluble protein, nitrate reductase and soil urease activities were improved over those of the no-drought treatment. Proteobacteria, Bacteroidota, Nitrospirota and Zixibacteria were the dominant flora related to N absorption. A total of 184 DMs (98 upregulated and 86 downregulated) were identified between low N with no drought (LN) and normal N with no drought (NN); 139 DMs (83 upregulated and 56 downregulated) were identified between high N with no drought (HN) and NN; 166 DMs (103 upregulated and 63 downregulated) were identified between low N with drought stress (LND) and normal N with drought stress (NND); and 124 DMs (71 upregulated and 53 downregulated) were identified between high N with drought stress (HND) and NND. Fatty acyl was the metabolite with the highest proportion. KEGG analysis showed that energy metabolism pathways, such as D-alanine metabolism and the phosphotransferase system (PTS), were enriched. We conclude that N-metabolism enzymes with higher activity and higher bacterial diversity have a significant effect on drought tolerance and nitrogen uptake in rice.

Metabolomic and transcriptomic investigation of the mechanism involved in enantioselective toxicity of imazamox in Lemna minor

Imazamox (IM) is a chiral pesticide that has been widely used in agriculture. Currently, few studies have investigated the toxicity mechanisms of imazamox to aquatic macrophyte from the enantiomer level. In this study, the enantioselective effects of IM on the toxicity and physiological and biochemical system of aquatic macrophyte Lemna minor were systematically investigated. Metabolomic and transcriptomic for Lemna minor were used to identify potential mechanisms of toxicity. 7 d EC₅₀s for racemic-, R-, and S-IM were 0.036, 0.035, and 0.203 mg/L, respectively, showing enantioselective toxicity. In addition, IM caused Lemna minor lipid peroxidation and antioxidant damage, and inhibited the activities of the target enzymes. Metabolomic and transcriptomic data indicated that R-IM interferenced differentially expressed genes and metabolites of Lemna minor which were enriched in carbon fixation during photosynthesis, glutathione metabolic pathway, pentose phosphate pathway, zeatin biosynthesis, and porphyrin and chlorophyll metabolism. S-IM affected phenylalanine metabolism, phenylpropanoid biosynthesis, zeatin biosynthesis and secondary metabolite biosynthesis. Racemic-IM influenced carbon fixation during operation, glutathione metabolic pathway, zeatin biosynthesis and pentose phosphate pathway. The results provide new insights into the enantioselective toxicity mechanisms of IM to Lemna minor, and lay the foundation for conducting environmental risk assessments.

Growth performance and nitrogen allocation within leaves of two poplar clones after exponential and conventional nitrogen applications

Populus species are fast growing with high N requirements; an optimum level of fertilization is necessary for high seedling quality and subsequent plantation productivity. In this study, the morphological and physiological responses of two poplar clones (XH and BL3) to exponential and conventional N dosages were investigated, with a specific focus on leaf traits, the photorespiratory N cycle, and the interconversion of amino acids within leaves. Results show that shoot height and leaf number exponentially increased with plant growth. Leaf area, chlorophyll concentration, and net photosynthetic rate significantly increased for both clones during N fertilization, with a significant difference only in leaf area of clone XH between exponential and conventional dosages. Leaf concentrations of free amino acids and soluble sugars were not different but soluble proteins and fatty acids were significantly different for clone XH between N dosages; the amino acids glutamate, alanine, and aspartic acid concentrations increased in exponentially fertilized seedlings compared to controls. Amino acids, including the composition concentration and activity of glutamic-oxalacetic and -pyruvic transaminase, and soluble sugars were significantly higher for clone BL3 in fertilized seedlings. Photorespiration (glycine and glycolate oxidase) and glutathione redox (oxidized glutathione) were affected by fertilization. The activities of key enzymes (glycolate oxidase, catalase, and γ-glutamate cysteine ligase) involved in photorespiration and glutathione metabolism were lower for clone XH with exponential fertilization. Phenylalanine catabolism was influenced by fertilization and the interaction, clone × fertilization, showing accumulation of phenylalanine and tyrosine but decreases in phenylalanine ammonialyase activity and flavonoid concentrations in leaves of fertilized seedlings. The results indicate that leaf area and the interconversion of amino acids through deamidation/transamination are key regulatory hubs in poplar acclimation to soil N availability.

Source-sink modifications affect leaf senescence and grain mass in wheat as revealed by proteomic analysis

BACKGROUND

The grain yield of cereals is determined by the synergistic interaction between source activity and sink capacity. However, source-sink interactions are far from being fully understood. Therefore, a field experiment was performed in wheat to investigate the responses of flag leaves and grains to sink/source manipulations.

RESULTS

Half-degraining delayed but partial defoliation enhanced leaf senescence. Sink/source manipulations influenced the content of reactive oxygen species in the flag leaf and the concentration of phytohormones, including cytokinins, indoleacetic 3-acid and jasmonic acid, in the flag leaves (LDef) and grains (GDef) in defoliated plants and flag leaves (LDG) and grain (GDG) in de-grained plants. Isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomic analysis indicated that at 16 days after manipulation, a total of 97 and 59 differentially expressed proteins (DEPs) from various functional categories were observed in the LDG and LDef groups, respectively, compared with the control, and 115 and 121 DEPs were observed in the GDG and GDef groups, respectively. The gene ontology annotation terms of the DEPs mainly included carbon fixation, hydrogen peroxide catabolic process, chloroplast and cytoplasm, oxidoreductase activity and glutamate synthase activity in the flag leaves of manipulated plants and organonitrogen compound metabolic process, cytoplasm, vacuolar membrane, CoA carboxylase activity, starch synthase activity and nutrient reservoir activity in the grains of manipulated plants. KEGG pathway enrichment analysis revealed that photosynthesis, carbon, nitrogen and pyruvate metabolism and glycolysis/gluconeogenesis were the processes most affected by sink/source manipulations. Sink/source manipulations affected the activities of amylase and proteinases and, ultimately, changed the mass per grain.

CONCLUSIONS

Manipulations to change the sink/source ratio affect hormone levels; hydrolytic enzyme activities; metabolism of carbon, nitrogen and other main compounds; stress resistance; and leaf senescence and thus influence grain mass.

Proteomic Analysis of Rice Subjected to Low Light Stress and Overexpression of OsGAPB Increases the Stress Tolerance

BACKGROUND

Light provides the energy for photosynthesis and determines plant morphogenesis and development. Low light compromises photosynthetic efficiency and leads to crop yield loss. It remains unknown how rice responds to low light stress at a proteomic level.

RESULTS

In this study, the quantitative proteomic analysis with isobaric tags for relative and absolute quantitation (iTRAQ) was used and 1221 differentially expressed proteins (DEPs) were identified from wild type rice plants grown in control or low light condition (17% light intensity of control), respectively. Bioinformatic analysis of DEPs indicated low light remarkably affects the abundance of chloroplastic proteins. Specifically, the proteins involved in carbon fixation (Calvin cycle), electron transport, and ATPase complex are severely downregulated under low light. Furthermore, overexpression of the downregulated gene encoding rice β subunit of glyceraldehyde-3-phosphate dehydrogenase (OsGAPB), an enzyme in Calvin cycle, significantly increased the CO₂ assimilation rate, chlorophyll content and fresh weight under low light conditions but have no obvious effect on rice growth and development under control light.

CONCLUSION

Our results revealed that low light stress on vegetative stage of rice inhibits photosynthesis possibly by decreasing the photosynthetic proteins and OsGAPB gene is a good candidate for manipulating rice tolerance to low light stress.