Soybean Metabolomics Based in Mass Spectrometry: Decoding the Plant's Signaling and Defense Responses under Biotic Stress

Metabolomics approach to understand molecular mechanisms involved in fungal pathogen-citrus pathosystems

Citrus is a crucial crop with a significant economic impact globally. However, postharvest decay caused by fungal pathogens poses a considerable threat, leading to substantial financial losses. Penicillium digitatum, Penicillium italicum, Geotrichum citri-aurantii and Phyllosticta citricarpa are the main fungal pathogens, causing green mold, blue mold, sour rot and citrus black spot diseases, respectively. The use of chemical fungicides as a control strategy in citrus raises concerns about food and environmental safety. Therefore, understanding the molecular basis of host-pathogen interactions is essential to find safer alternatives. This review highlights the potential of the metabolomics approach in the search for bioactive compounds involved in the pathogen-citrus interaction, and how the integration of metabolomics and genomics contributes to the understanding of secondary metabolites associated with fungal virulence and the fungal infection mechanisms. Our goal is to provide a pipeline combining metabolomics and genomics that can effectively guide researchers to perform studies aiming to contribute to the understanding of the fundamental chemical and biochemical aspects of pathogen-host interactions, in order to effectively develop new alternatives for fungal diseases in citrus cultivation. We intend to inspire the scientific community to question unexplored biological systems, and to employ diverse analytical approaches and metabolomics techniques to address outstanding questions about the non-studied pathosystems from a chemical biology perspective.

Regulation of seed traits in soybean

Soybean (Glycine max) is an essential economic crop that provides vegetative oil and protein for humans, worldwide. Increasing soybean yield as well as improving seed quality is of great importance. Seed weight/size, oil and protein content are the three major traits determining seed quality, and seed weight also influences soybean yield. In recent years, the availability of soybean omics data and the development of related techniques have paved the way for better research on soybean functional genomics, providing a comprehensive understanding of gene functions. This review summarizes the regulatory genes that influence seed size/weight, oil content and protein content in soybean. We also provided a general overview of the pleiotropic effect for the genes in controlling seed traits and environmental stresses. Ultimately, it is expected that this review will be beneficial in breeding improved traits in soybean.

Dissolved organic matter transformation mechanisms and process optimization of wastewater sludge hydrothermal humification treatment for producing plant biostimulants

Understanding the composition, transformation and bioactivity of dissolved organic matter (DOM) at the molecular level is crucial for investigating the hydrothermal humification process of wastewater sludge and producing ecological fertilizers. In this study, DOM transformation pathways under alkali-thermal humification treatment (AHT) were characterized by Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) in conjunction with molecular reaction network analysis. The effects of DOM on plant growth were examined using hydroponics and transcriptomic analysis. In the wastewater sludge humification process, AHT produced maximum amounts of protein (3260.56 mg/L) and humic acid (5788.24 mg/L) after 12 h. FT-ICR MS results indicated that protein-like structures were prone to continuous oxidation and were ultimately transformed into aromatic N-containing compounds resembling humic substances. Several reactive fragments (such as -C₂H₂O₂, -C₃H₄O₂, and -C₄H₆O₂) formed by the Maillard reaction (MR) were identified as potential precursors to humic acid (HA). In terms of biological effects, DOM_12h showed the highest rice germination and growth activity, whereas that produced by AHT for a longer period (> 12 h) displayed phytotoxicity owing to the accumulation of toxic substances. Plant biostimulants (such as amino acids and HAs) in DOM improved energy metabolism and carbohydrate storage in rice seedlings by upregulating the "starch and sucrose metabolism" pathways. Toxic substances (such as pyrrole, pyridine, and melanoidin) in DOM can activate cell walls formation to inhibit abiotic stimuli in rice seedlings through the biosynthesis of phenylpropanoid pathway. These findings provide a theoretical basis for optimizing sludge hydrothermal humification and recovering high-quality liquid fertilizers.

Genetic regulatory networks of soybean seed size, oil and protein contents

As a leading oilseed crop that supplies plant oil and protein for daily human life, increasing yield and improving nutritional quality (high oil or protein) are the top two fundamental goals of soybean breeding. Seed size is one of the most critical factors determining soybean yield. Seed size, oil and protein contents are complex quantitative traits governed by genetic and environmental factors during seed development. The composition and quantity of seed storage reserves directly affect seed size. In general, oil and protein make up almost 60% of the total storage of soybean seed. Therefore, soybean's seed size, oil, or protein content are highly correlated agronomical traits. Increasing seed size helps increase soybean yield and probably improves seed quality. Similarly, rising oil and protein contents improves the soybean's nutritional quality and will likely increase soybean yield. Due to the importance of these three seed traits in soybean breeding, extensive studies have been conducted on their underlying quantitative trait locus (QTLs) or genes and the dissection of their molecular regulatory pathways. This review summarized the progress in functional genome controlling soybean seed size, oil and protein contents in recent decades, and presented the challenges and prospects for developing high-yield soybean cultivars with high oil or protein content. In the end, we hope this review will be helpful to the improvement of soybean yield and quality in the future breeding process.

Responses of differential metabolites and pathways to high temperature in cucumber anther

Cucumber is one of the most important vegetable crops, which is widely planted all over the world. Cucumber always suffers from high-temperature stress in South China in summer. In this study, liquid chromatography-mass spectrometry (LC-MS) analysis was used to study the differential metabolites of cucumber anther between high-temperature (HT) stress and normal condition (CK). After HT, the pollen fertility was significantly reduced, and abnormal anther structures were observed by the paraffin section. In addition, the metabolomics analysis results showed that a total of 125 differential metabolites were identified after HT, consisting of 99 significantly upregulated and 26 significantly downregulated metabolites. Among these differential metabolites, a total of 26 related metabolic pathways were found, and four pathways showed significant differences, namely, porphyrin and chlorophyll metabolism; plant hormone signal transduction; amino sugar and nucleotide sugar metabolism; and glycine, serine, and threonine metabolism. In addition, pollen fertility was decreased by altering the metabolites of plant hormone signal transduction and amino acid and sugar metabolism pathway under HT. These results provide a comprehensive understanding of the metabolic changes in cucumber anther under HT.

Functional characterization of Cinnamate 4-hydroxylase gene family in soybean (Glycine max)

Cinnamate 4-hydroxylase (C4H) is the first key cytochrome P450 monooxygenase (P450) enzyme in the phenylpropanoid pathway. It belongs to the CYP73 family of P450 superfamily, and catalyzes the conversion of trans-cinnamic acid to p-coumaric acid. Since p-coumaric acid serves as the precursor for the synthesis of a wide variety of metabolites involved in plant development and stress resistance, alteration in the expression of soybean C4H genes is expected to affect the downstream metabolite levels, and its ability to respond to stress. In this study, we identified four C4H genes in the soybean genome that are distributed into both class I and class II CYP73 family. GmC4H2, GmC4H14 and GmC4H20 displayed tissue- and developmental stage-specific gene expression patterns with their transcript accumulation at the highest level in root tissues. GmC4H10 appears to be a pseudogene as its transcript was not detected in any soybean tissues. Furthermore, protein homology modelling revealed substrate docking only for GmC4H2, GmC4H14 and GmC4H20. To demonstrate the function of GmC4Hs, we modified a cloning vector for the heterologous expression of P450s in yeast, and used it for microsomal protein production and enzyme assay. Our results confirmed that GmC4H2, GmC4H14 and GmC4H20 contain the ability to hydroxylate trans-cinnamic acid with varying efficiencies.

Metabolite Profiling of Soy By-Products: A Comprehensive Approach

Soy is the major oilseed crop as soybeans are widely used to produce biofuel, food, and feed. Other parts of the plant are left on the ground after harvest. The accumulation of such by-products on the soil can cause environmental problems. This work presents for the first time a comprehensive metabolite profiling of soy by-products collected directly from the ground just after mechanical harvesting. A two-liquid-phase extraction using n-heptane and EtOH-H2O 7:3 (v/v) provided extracts with complete characterization by gas chromatography and ultra-high-performance liquid chromatography both coupled to time-of-flight mass spectrometry. A total of 146 metabolites, including flavones, flavonols, isoflavonoids, fatty acids, steroids, mono-, sesqui-, di-, and triterpenoids, were tentatively identified in soy by-products and soybeans. These proved to be sources of a wide range of bioactive metabolites, thus suggesting that they could be valorized while reducing potential environmental damage in line with a circular economy model.