Effects of Fe and Mn deficiencies on the protein profiles of tomato (Solanum lycopersicum) xylem sap as revealed by shotgun analyses

Micronutrient deficiency-induced oxidative stress in plants

Micronutrients like iron (Fe), zinc (Zn), copper (Cu), manganese (Mn), boron (B), nickel (Ni), and molybdenum (Mo) perform significant roles in the regulation of plant metabolism, growth, and development. Micronutrients, namely Fe, Zn, Cu, Mn, and Ni, are involved in oxidative stress and antioxidant defense as they are cofactors or activators of various antioxidant enzymes, viz., superoxide dismutase (Fe, Cu/Zn, Mn, and Ni), catalase (Fe), and ascorbate peroxidase (Fe). An effort has been made to incorporate recent advances along with classical work done on the micronutrient deficiency-induced oxidative stress and associated antioxidant responses of plants. Deficiency of a micronutrient produces ROS in the cellular compartments. Enzymatic and non-enzymatic antioxidant defense systems are often modulated by micronutrient deficiency to regulate redox balance and scavenge deleterious ROS for the safety of cellular constituents. ROS can strike cellular constituents such as lipids, proteins, and nucleic acids and can destruct cellular membranes and proteins. ROS might act as a signaling molecule and activate the antioxidant proteins by interacting with signaling partners such as respiratory burst oxidase homolog (RBOH), G-proteins, Ca2+, mitogen activated protein kinases (MAPKs), and various transcription factors (TFs). Opinions on probable ROS signaling under micronutrient deficiency have been described in this review. However, further research is required to decipher micronutrient deficiency-induced ROS generation, perception, and associated downstream signaling events, leading to the development of antioxidant responses in plants.

Expeditious profiling of polycyclic aromatic hydrocarbons transport and obstruction mechanisms in crop xylem sap proteins via proteomics and molecular docking

Polycyclic aromatic hydrocarbons (PAHs) pose significant environmental risks due to their toxicity and carcinogenic properties. This research seeks to pinpoint protein targets in crop xylem sap related to PAH contamination and delve into their protein-ligand interactions using computational tools. Proteomic assessment revealed differentially expressed proteins (DEPs), which were subjected to virtual high-throughput screening. Notably, the phenanthrene's influence on xylem sap proteins in maize and wheat was more pronounced than in soybean, with DEPs expression peak at 24 h post-treatment. Maize DEPs were predominantly associated with lipid biosynthesis. Phenanthrene impacted cell membrane hydrophobicity, limiting PAH adsorption and decreasing its concentration in maize xylem sap. Wheat DEPs exhibited an increase in ABC transporters after 24 h of phenanthrene exposure. ABC transporters interacted with stress-responsive proteins like C6TIY1-Co-chaperone p23 and others that either facilitate or inhibit PAH transport, including Indeno[1,2,3-cd]Pyrene and C6TIY1-Co-chaperone protein p23. Both maize and wheat created high-affinity complexes between specific proteins and PAHs, influencing their transport. This study provides insights into the mechanisms of PAH regulation and movement within plant xylem.

Metabolic profiles in the xylem sap of Brassica juncea exposed to cadmium

Metabolic profiles in xylem sap are considered a fundamental mechanism for Cadmium (Cd) detoxification in plants. However, the metabolic mechanism of Brassica juncea xylem sap in response to Cd is still unclear. Here, we investigated the effects on the metabolomics of B. juncea xylem sap treated with Cd at different times by utilizing a nontargeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomics method for further elucidating the response mechanism of Cd exposure. The findings indicated that 48 h and 7 days Cd exposure caused significant differences in metabolic profiles of the B. juncea xylem sap. Those differential metabolites are primarily involved in amino acids, organic acids, lipids, and carbohydrates, and most of them were downregulated, which played essential roles in response to Cd stress. Furthermore, B. juncea xylem sap resisted 48-h Cd exposure via regulation of glycerophospholipid metabolism, carbon metabolism, aminoacyl-tRNA biosynthesis, glyoxylate and dicarboxylate metabolism, linoleic acid metabolism, C5-branched dibasic acid metabolism, alpha-linolenic acid metabolism, cyanoamino acid metabolism, ABC transporters, biosynthesis of amino acids, and pyrimidine metabolism; whereas alpha-linolenic acid metabolism, glycerophospholipid metabolism, photosynthesis, and oxidative phosphorylation were regulated for resisting 7-day Cd exposure.

Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato

The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato germplasms to subdue biotic and abiotic stresses. Proteomic investigations within a span of few decades have assisted in consolidating the functional genomics and transcriptomic research. However, due to the volatility and dynamicity of proteins in the regulation of various biosynthetic pathways, there is a need for continuing research in the field of proteomics to establish a network that could enable a more comprehensive understanding of tomato growth and development. With this view, we provide a comprehensive review of proteomic studies conducted on the tomato plant in past years, which will be useful for future breeders and researchers working to improve the tomato crop.

Mechanistic insights into phenanthrene acropetal translocation via wheat xylem: Separation and identification of transfer proteins

Polycyclic aromatic hydrocarbons (PAHs) have the potential to cause cancer, teratogenicity, and mutagenesis in humans. Long-term plant safe production relies on how PAHs are transported and coordinated across organs. However, the acropetal transfer mechanism of PAHs in staple crop stems, particularly in xylem, a critical path, is unknown. Herein, we first confirmed the presence of specific interaction between the proteins and phenanthrene by employing the magnetic phenanthrene-bound bead immunoassay and label free liquid chromatograph mass spectrometer (LC-MS/MS), suggesting that peroxidase (uniprot accession: A0A3B5XXD0) and unidentified proteins (uniprot accession: A0A3B6LUC6) may function as the carriers to load and acropetally translocate phenanthrene (a model PAH) in wheat xylem. This specified binding of protein-phenanthrene may form through hydrophobic interactions in the conservative binding region, as revealed by protein structural investigations and molecular docking. To further investigate the role of these proteins in phenanthrene solubilization, phenanthrene exposure was conducted: a substantial quantity of peroxidase was produced; an unusually high expression of uncharacterized proteins was observed, indicating their positive effects in the acropetal transfer of phenanthrene in wheat xylem. These data confirmed that the two proteins are crucial in the solubilization of phenanthrene in wheat xylem sap. Our findings provide fresh light on the molecular mechanism of PAH loading in plant xylem and techniques for ensuring the security of staple crops and improving the efficacy of phytoremediation in a PAH-contaminated environment.

Sec24C mediates a Golgi-independent trafficking pathway that is required for tonoplast localisation of ABCC1 and ABCC2

Protein sorting is an essential biological process in all organisms. Trafficking membrane proteins generally relies on the sorting machinery of the Golgi apparatus. However, many proteins have been found to be delivered to target locations via Golgi-independent pathways, but the mechanisms underlying this delivery system remain unknown. Here, we report that Sec24C mediates the direct secretory trafficking of the phytochelatin transporters ABCC1 and ABCC2 from the endoplasmic reticulum (ER) to prevacuolar compartments (PVCs) in Arabidopsis thaliana. Genetic analysis showed that the sec24c mutants are hypersensitive to cadmium (Cd) and arsenic (As) treatments due to mislocalisation of ABCC1 and ABCC2, which results in defects in the vacuole compartmentalisation of the toxic metals. Furthermore, we found that Sec24C recognises ABCC1 and ABCC2 through direct interactions to mediate their exit from the ER to PVCs, which is independent of brefeldin A-sensitive post-Golgi trafficking pathway. These findings expand our understanding of Golgi-independent trafficking, which also provide key insights regarding the mechanism of tonoplast protein sorting and open a new perspective on the function of Sec24 proteins.

Effects of Fe and Mn Deficiencies on the Root Protein Profiles of Tomato (Solanum lycopersicum) Using Two-Dimensional Electrophoresis and Label-Free Shotgun Analyses

Iron (Fe) and manganese (Mn) are two essential elements for plants that compete for the same uptake transporters and show conflicting interactions at the regulatory level. In order to understand the differential response to both metal deficiencies in plants, two proteomic techniques (two-dimensional gel electrophoresis and label-free shotgun) were used to study the proteome profiles of roots from tomato plants grown under Fe or Mn deficiency. A total of 119 proteins changing in relative abundance were confidently quantified and identified, including 35 and 91 in the cases of Fe deficiency and Mn deficiency, respectively, with 7 of them changing in both deficiencies. The identified proteins were categorized according to function, and GO-enrichment analysis was performed. Data showed that both deficiencies provoked a common and intense cell wall remodelling. However, the response observed for Fe and Mn deficiencies differed greatly in relation to oxidative stress, coumarin production, protein, nitrogen, and energy metabolism.

Sap Analysis: A Powerful Tool for Monitoring Plant Nutrition

Horticultural crop production is moving towards an era of higher nutrient use efficiency since nutrient deficiencies can reduce plant growth, productivity, and quality, and overfertilization can cause environmental pollution. Rapid nutrient concentration diagnostic is essential to minimize the negative effects of Huanglongbing (HLB) or citrus greening in citrus by providing the required nutrients before deficiency symptoms appear, reducing the impact of the disease on crop production. Sap analysis is an additional tool for fine-tuning nutrient applications in citrus. The main objective of this paper is to review the different methodologies and results obtained with sap analysis, considering its potential application in citrus production. Results from other crops show the pros and cons of using this tool. Substantial research has been conducted on vegetables and greenhouse crops, but few studies are available on perennial species such as citrus. Inconsistency in the extraction and analysis methods and the lack of specific sufficiency ranges for citrus open the path for further studies. Along with soil and leaf analyses, sap analysis is a complementary technique that can improve nutrient use efficiency in citrus production. Moreover, sap analysis has the potential to optimize fertilizer application, minimize environmental impacts and improve sustainability.

Foliar application of 3-hydroxy-4-pyridinone Fe-chelate [Fe(mpp)3 ] induces responses at the root level amending iron deficiency chlorosis in soybean

Iron (Fe) deficiency chlorosis (IDC) affects the growth of several crops, especially when growing in alkaline soils. The application of synthetic Fe-chelates is one of the most commonly used strategies in IDC amendment, despite their associated negative environmental impacts. In a previous work, the Fe-chelate tris(3-hydroxy-1-(H)-2-methyl-4-pyridinonate) iron(III) [Fe(mpp)3 ] has shown great potential for alleviating IDC in soybean (Glycine max) in the early stages of plant development under hydroponic conditions. Herein, its efficacy was verified under soil conditions in soybean grown from seed to full maturity. Chlorophyll levels, plant growth, root and shoot mineral accumulation (K, Mg, Ca, Na, P, Mn, Zn, Ni, and Co) and FERRITIN expression were accessed at V5 phenological stage. Compared to a commonly used Fe chelate, FeEDDHA, supplementation with [Fe(mpp)3 ] led to a 29% higher relative chlorophyll content, 32% higher root biomass, 36% higher trifoliate Fe concentration, and a twofold increase in leaf FERRITIN gene expression. [Fe(mpp)3 ] supplementation also resulted in increased accumulation of P, K, Zn, and Co. At full maturity, the remaining plants were harvested and [Fe(mpp)3 ] application led to a 32% seed yield increase when compared to FeEDDHA. This is the first report on the use of [Fe(mpp)3 ] under alkaline soil conditions for IDC correction, and we show that its foliar application has a longer-lasting effect than FeEDDHA, induces efficient root responses, and promotes the uptake of other nutrients.

Unraveling the Roles of Vascular Proteins Using Proteomics

Vascular bundles play important roles in transporting nutrients, growth signals, amino acids, and proteins between aerial and underground tissues. In order to understand these sophisticated processes, a comprehensive analysis of the roles of the components located in the vascular tissues is required. A great deal of data has been obtained from proteomic analyses of vascular tissues in plants, which mainly aim to identify the proteins moving through the vascular tissues. Here, different aspects of the phloem and xylem proteins are reviewed, including their collection methods, and their main biological roles in growth, and biotic and abiotic stress responses. The study of vascular proteomics shows great potential to contribute to our understanding of the biological mechanisms related to development and defense in plants.

Effects of Excess Manganese on the Xylem Sap Protein Profile of Tomato (Solanum lycopersicum) as Revealed by Shotgun Proteomic Analysis

Metal toxicity is a common problem in crop species worldwide. Some metals are naturally toxic, whereas others such as manganese (Mn) are essential micro-nutrients for plant growth but can become toxic when in excess. Changes in the composition of the xylem sap, which is the main pathway for ion transport within the plant, is therefore vital to understanding the plant's response(s) to metal toxicity. In this study we have assessed the effects of exposure of tomato roots to excess Mn on the protein profile of the xylem sap, using a shotgun proteomics approach. Plants were grown in nutrient solution using 4.6 and 300 µM MnCl2 as control and excess Mn treatments, respectively. This approach yielded 668 proteins reliably identified and quantified. Excess Mn caused statistically significant (at p ≤ 0.05) and biologically relevant changes in relative abundance (≥2-fold increases or ≥50% decreases) in 322 proteins, with 82% of them predicted to be secretory using three different prediction tools, with more decreasing than increasing (181 and 82, respectively), suggesting that this metal stress causes an overall deactivation of metabolic pathways. Processes most affected by excess Mn were in the oxido-reductase, polysaccharide and protein metabolism classes. Excess Mn induced changes in hydrolases and peroxidases involved in cell wall degradation and lignin formation, respectively, consistent with the existence of alterations in the cell wall. Protein turnover was also affected, as indicated by the decrease in proteolytic enzymes and protein synthesis-related proteins. Excess Mn modified the redox environment of the xylem sap, with changes in the abundance of oxido-reductase and defense protein classes indicating a stress scenario. Finally, results indicate that excess Mn decreased the amounts of proteins associated with several signaling pathways, including fasciclin-like arabinogalactan-proteins and lipids, as well as proteases, which may be involved in the release of signaling peptides and protein maturation. The comparison of the proteins changing in abundance in xylem sap and roots indicate the existence of tissue-specific and systemic responses to excess Mn. Data are available via ProteomeXchange with identifier PXD021973.

Proteomic Approaches to Identify Cold-Regulated Plasma Membrane Proteins

Plasma membrane is the primary determinant of freezing tolerance in plants because of its central role in freeze-thaw cycle. Changes in plasma membrane protein composition have been one of the major research areas in plant cold acclimation. To obtain comprehensive profiles of the plasma membrane proteomes and their changes during the cold acclimation process, a plasma membrane purification method using a dextran-polyethylene glycol two polymer system and a mass spectrometry-based shotgun proteomics method using nano-LC-MS/MS for the plasma membrane proteins are described. The proteomic results obtained are further applied to label-free protein semiquantification.

Proteomic changes in the xylem sap of Brassica napus under cadmium stress and functional validation

BACKGROUND

The xylem sap of vascular plants primarily transports water and mineral nutrients from the roots to the shoots and also transports heavy metals such as cadmium (Cd). Proteomic changes in xylem sap is an important mechanism for detoxifying Cd by plants. However, it is unclear how proteins in xylem sap respond to Cd. Here, we investigated the effects of Cd stress on the xylem sap proteome of Brassica napus using a label-free shotgun proteomic approach to elucidate plant response mechanisms to Cd toxicity.

RESULTS

We identified and quantified 672 proteins; 67% were predicted to be secretory, and 11% (73 proteins) were unique to Cd-treated samples. Cd stress caused statistically significant and biologically relevant abundance changes in 28 xylem sap proteins. Among these proteins, the metabolic pathways that were most affected were related to cell wall modifications, stress/oxidoreductases, and lipid and protein metabolism. We functionally validated a plant defensin-like protein, BnPDFL, which belongs to the stress/oxidoreductase category, that was unique to the Cd-treated samples and played a positive role in Cd tolerance. Subcellular localization analysis revealed that BnPDFL is cell wall-localized. In vitro Cd-binding assays revealed that BnPDFL has Cd-chelating activity. BnPDFL heterologous overexpression significantly enhanced Cd tolerance in E. coli and Arabidopsis. Functional disruption of Arabidopsis plant defensin genes AtPDF2.3 and AtPDF2.2, which are mainly expressed in root vascular bundles, significantly decreased Cd tolerance.

CONCLUSIONS

Several xylem sap proteins in Brassica napus are differentially induced in response to Cd treatment, and plant defensin plays a positive role in Cd tolerance.

Identification, expression analysis, and molecular modeling of Iron-deficiency-specific clone 3 (Ids3)-like gene in hexaploid wheat

Graminaceous plants secrete hydroxylated phytosiderophores encoded by the genes iron-deficiency-specific clone 2 (Ids2) and iron-deficiency-specific clone 3 (Ids3). An effort was made to identify a putative ortholog of Hodeum vulgare Ids3 gene in hexaploid wheat. The protein structure of TaIDS3 was modeled using homology modeling and structural behavior of modeled structure was analyzed at 20 ns. The simulation trajectory using molecular dynamics simulation suggested the model to be stable with no large fluctuations in residues and local domain level RMSF values (< 2.4 Å). In addition, the ProFunc results also predict the functional similarity between the proteins of HvIDS3 and its wheat ortholog (TaIDS3). The TaIds3 gene was assigned to the telomeric region of chromosome arm 7AS which supports the results obtained through bioinformatics analysis. The relative expression analysis of TaIds3 indicated that the detectable expression of TaIds3 is induced after 5th day of Fe starvation and increases gradually up to 15th day, and thereafter, it decreases until 35th day of Fe-starvation. This reflects that Fe deficiency directly regulates the induction of TaIds3 in the roots of hexaploid wheat. The identification of HvIds3-like gene in wheat has opened up new opportunities to enhance the nutrient quality in wheat through biofortification program.

Data on xylem sap proteins from Mn- and Fe-deficient tomato plants obtained using shotgun proteomics

This article contains consolidated proteomic data obtained from xylem sap collected from tomato plants grown in Fe- and Mn-sufficient control, as well as Fe-deficient and Mn-deficient conditions. Data presented here cover proteins identified and quantified by shotgun proteomics and Progenesis LC-MS analyses: proteins identified with at least two peptides and showing changes statistically significant (ANOVA; p ≤ 0.05) and above a biologically relevant selected threshold (fold ≥ 2) between treatments are listed. The comparison between Fe-deficient, Mn-deficient and control xylem sap samples using a multivariate statistical data analysis (Principal Component Analysis, PCA) is also included. Data included in this article are discussed in depth in the research article entitled “Effects of Fe and Mn deficiencies on the protein profiles of tomato (Solanum lycopersicum) xylem sap as revealed by shotgun analyses” [1]. This dataset is made available to support the cited study as well to extend analyses at a later stage.