Optimization of Targeted Plant Proteomics Using Liquid Chromatography with Tandem Mass Spectrometry (LC-MS/MS)

Multi-omic applications for understanding and enhancing tropical fruit flavour

Consumer trends towards nutrient-rich foods are contributing to global increasing demand for tropical fruit. However, commercial cultivars in the breeding pipeline that are tailored to meet market demand are at risk of possessing reduced fruit flavour qualities. This stems from recurrent prioritised selection for superior agronomic traits and not fruit flavour, which may in turn reduce consumer satisfaction. There is realisation that fruit quality traits, inclusive of flavour, must be equally selected for; but currently, there are limited tools and resources available to select for fruit flavour traits, particularly in tropical fruit species. Although sugars, acids, and volatile organic compounds are known to define fruit flavour, the specific combinations of these, that result in defined consumer preferences, remain unknown for many tropical fruit species. To define and include fruit flavour preferences in selective breeding, it is vital to determine the metabolites that underpin them. Then, objective quantitative analysis may be implemented instead of solely relying on human sensory panels. This may lead to the development of selective genetic markers through integrated omics approaches that target biosynthetic pathways of flavour active compounds. In this review, we explore progress in the development of tools to be able to strategically define and select for consumer-preferred flavour profiles in the breeding of new cultivars of tropical fruit species.

Integrating Targeted Metabolomics and Targeted Proteomics to Study the Responses of Wheat Plants to Engineered Nanomaterials

This manuscript presents a multiomics investigation into the metabolic and proteomic responses of wheat to molybdenum (Mo)- and copper (Cu)-based engineered nanomaterials (ENMs) exposure via root and leaf application methods. Wheat plants underwent a four-week growth period with a 16 h photoperiod (light intensity set at 150 μmol·m-2·s-1), at 22 °C and 60% humidity. Six distinct treatments were applied, including control conditions alongside exposure to Mo- and Cu-based ENMs through both root and leaf routes. The exposure dosage amounted to 6.25 mg of the respective element per plant. An additional treatment with a lower dose (0.6 mg Mo/plant) of Mo ENM exclusively through the root system was introduced upon the detection of phytotoxicity. Utilizing LC-MS/MS analysis, 82 metabolites across various classes and 24 proteins were assessed in different plant tissues (roots, stems, leaves) under diverse treatments. The investigation identified 58 responsive metabolites and 19 responsive proteins for Cu treatments, 71 responsive metabolites, and 24 responsive proteins for Mo treatments, mostly through leaf exposure for Cu and root exposure for Mo. Distinct tissue-specific preferences for metabolite accumulation were revealed, highlighting the prevalence of organic acids and fatty acids in stem or root tissues, while sugars and amino acids were abundant in leaves, mirroring their roles in energy storage and photosynthesis. Joint-pathway analysis was conducted and unveiled 23 perturbed pathways across treatments. Among these, Mo exposure via roots impacted all identified pathways, whereas exposure via leaf affected 15 pathways, underscoring the reliance on exposure route of metabolic and proteomic responses. The coordinated response observed in protein and metabolite concentrations, particularly in amino acids, highlighted a dynamic and interconnected proteomic-to-metabolic-to-proteomic relationship. Furthermore, the contrasting expression patterns observed in glutamate dehydrogenase (upregulation at 1.38 ≤ FC ≤ 1.63 with high Mo dose, and downregulation at 0.13 ≤ FC ≤ 0.54 with low Mo dose) and its consequential impact on glutamine expression (7.67 ≤ FC ≤ 39.60 with high Mo dose and 1.50 ≤ FC ≤ 1.95 with low Mo dose) following Mo root exposure highlighted dose-dependent regulatory trends influencing proteins and metabolites. These findings offer a multidimensional understanding of plant responses to ENMs exposure, guiding agricultural practices and environmental safety protocols while advancing knowledge on nanomaterial impacts on plant biology.

Critical Review: Uptake and Translocation of Organic Nanodelivery Vehicles in Plants

Nanodelivery vehicles (NDVs) are engineered nanomaterials (ENMs) that, within the agricultural sector, have been investigated for their ability to improve uptake and translocation of agrochemicals, control release, or target specific tissues or subcellular compartments. Both inorganic and organic NDVs have been studied for agrochemical delivery in the literature, but research on the latter has been slower to develop than the literature on the former. Since the two classes of nanomaterials exhibit significant differences in surface chemistry, physical deformability, and even colloidal stability, trends that apply to inorganic NDVs may not hold for organic NDVs, and vice versa. We here review the current literature on the uptake, translocation, biotransformation, and cellular and subcellular internalization of organic NDVs in plants following foliar or root administration. A background on nanomaterials and plant physiology is provided as a leveling ground for researchers in the field. Trends in uptake and translocation are examined as a function of NDV properties and compared to those reported for inorganic nanomaterials. Methods for assessing fate and transport of organic NDVs in plants (a major bottleneck in the field) are discussed. We end by identifying knowledge gaps in the literature that must be understood in order to rationally design organic NDVs for precision agrochemical nanodelivery.

Assessing the Impacts of Cu and Mo Engineered Nanomaterials on Crop Plant Growth Using a Targeted Proteomics Approach

In this study, we investigated the effects of molybdenum (Mo)-based nanofertilizer and copper (Cu)-based nanopesticide exposure on wheat through a multifaceted approach, including physiological measurements, metal uptake and translocation analysis, and targeted proteomics analysis. Wheat plants were grown under a 16 h photoperiod (light intensity 150 μmol·m-2·s-1) for 4 weeks at 22 °C and 60% humidity with 6 different treatments, including control, Mo, and Cu exposure through root and leaf. The exposure dose was 6.25 mg of element per plant through either root or leaf. An additional low-dose (0.6 mg Mo/plant) treatment of Mo through root was added after phytotoxicity was observed. Using targeted proteomics approach, 24 proteins involved in 12 metabolomic pathways were quantitated to understand the regulation at the protein level. Mo exposure, particularly through root uptake, induced significant upregulation of 16 proteins associated with 11 metabolic pathways, with the fold change (FC) ranging from 1.28 to 2.81. Notably, a dose-dependent response of Mo exposure through the roots highlighted the delicate balance between nutrient stimulation and toxicity as a high Mo dose led to robust protein upregulation but also resulted in depressed physiological measurements, while a low Mo dose resulted in no depression of physiological measurements but downregulations of proteins, especially in the first leaf (0.23 < FC < 0.68) and stem (0.13 < FC < 0.68) tissues. Conversely, Cu exposure exhibited tissue-specific effects, with pronounced downregulation (18 proteins involved in 11 metabolic pathways) particularly in the first leaf tissues (root exposure: 0.35 < FC < 0.74; leaf exposure: 0.49 < FC < 0.72), which indicated the quick response of plants to Cu-induced stress in the early stage of exposure. By revealing the complexities of plants' response to engineered nanomaterials at both physiological and molecular levels, this study provides insights for optimizing nutrient management practices in crop production and advancing toward sustainable agriculture.