Proteomic analysis on roots of Oenothera glazioviana under copper-stress conditions

Proteomic analysis reveals the roles of silicon in mitigating glyphosate-induced toxicity in Brassica napus L

Glyphosate (Gly) is a widely used herbicide for weed control in agriculture, but it can also adversely affect crops by impairing growth, reducing yield, and disrupting nutrient uptake, while inducing toxicity. Therefore, adopting integrated eco-friendly approaches and understanding the mechanisms of glyphosate tolerance in plants is crucial, as these areas remain underexplored. This study provides proteome insights into Si-mediated improvement of Gly-toxicity tolerance in Brassica napus. The proteome analysis identified a total of 4,407 proteins, of which 594 were differentially abundant, including 208 up-regulated and 386 down-regulated proteins. These proteins are associated with diverse biological processes in B. napus, including energy metabolism, antioxidant activity, signal transduction, photosynthesis, sulfur assimilation, cell wall functions, herbicide tolerance, and plant development. Protein-protein interactome analyses confirmed the involvement of six key proteins, including L-ascorbate peroxidase, superoxide dismutase, glutaredoxin-C2, peroxidase, glutathione peroxidase (GPX) 2, and peptide methionine sulfoxide reductase A3 which involved in antioxidant activity, sulfur assimilation, and herbicide tolerance, contributing to the resilience of B. napus against Gly toxicity. The proteomics insights into Si-mediated Gly-toxicity mitigation is an eco-friendly approach, and alteration of key molecular processes opens a new perspective of multi-omics-assisted B. napus breeding for enhancing herbicide resistant oilseed crop production.

Identification of the succinate-CoA ligase protein gene family reveals that TaSUCL1-1 positively regulate cadmium resistance in wheat

The Succinate-CoA ligase (SUCL1) gene family is involved in energy metabolism, phytohormone signaling, and plant growth, development, and tolerance to stress. This is the first study to analyze the SUCL1 gene family in wheat (Triticum aestivum). 17 TaSUCL1 genes were identified in the complete genome sequence and classified into five subfamilies based on related genes found in three other species. The 17 TaSUCL1 genes were unevenly distributed across 11 chromosomes, and the collinearity of these genes was further investigated. Through using real-time qPCR (RT-qPCR) analysis, we identified the expression patterns of the TaSUCL1 genes under various tissues and different heavy metal stress conditions. The functions of selected TaSUCL1-1 gene were investigated by RNA interference (RNAi). This study provided a comprehensive analysis of the TaSUCL1 gene family. Within the TaSUCL1 genes, the exon-intron structure and motif composition exhibited significant similarity among members of the same evolutionary branch. Homology analysis and phylogenetic comparison of the SUCL1 genes in different plants offered valuable insights for studying the evolutionary characteristics of the SUCL1 genes. The expression levels of the TaSUCL1 genes in different tissues and under various metal stress conditions reveal its important role in plant growth and development. Gene function analysis demonstrated that TaSUCL1-1 silenced wheat plants exhibited a decrease in the total cadmium (Cd) concentrations and gene expression levels compared to the wild type (WT). Additionally, TaSUCL1-1 belonging to class c physically interacts with the β-amylase protein TaBMY1 as verified by yeast two-hybridization. This research provides a useful resource for further study of the function and molecular genetic mechanism of the SUCL1 gene family members.

Proteome insights of citric acid-mediated cadmium toxicity tolerance in Brassica napus L

Cadmium (Cd) is a toxic substance that is uptake by plants from soils, Cd easily transfers into the food chain. Considering global food security, eco-friendly, cost-effective, and metal detoxification strategies are highly demandable for sustainable food crop production. The purpose of this study was to investigate how citric acid (CA) alleviates or tolerates Cd toxicity in Brassica using a proteome approach. In this study, the global proteome level was significantly altered under Cd toxicity with or without CA supplementation in Brassica. A total of 4947 proteins were identified using the gel-free proteome approach. Out of these, 476 proteins showed differential abundance between the treatment groups, wherein 316 were upregulated and 160 were downregulated. The gene ontology analysis reveals that differentially abundant proteins were involved in different biological processes including energy and carbohydrate metabolism, CO2 assimilation and photosynthesis, signal transduction and protein metabolism, antioxidant defense, heavy metal detoxification, plant development, and cytoskeleton and cell wall structure in Brassica leaves. Interestingly, several candidate proteins such as superoxide dismutase (A0A078GZ68) L-ascorbate peroxidase 3 (A0A078HSG4), glutamine synthetase (A0A078HLB2), glutathione S-transferase DHAR1 (A0A078HPN8), glutamine synthetase (A0A078HLB2), cysteine synthase (A0A078GAD3), S-adenosylmethionine synthase 2 (A0A078JDL6), and thiosulfate/3-mercaptopyruvate sulfur transferase 2 (A0A078H905) were involved in antioxidant defense system and sulfur assimilation-involving Cd-detoxification process in Brassica. These findings provide new proteome insights into CA-mediated Cd-toxicity alleviation in Brassica, which might be useful to oilseed crop breeders for enhancing heavy metal tolerance in Brassica using the breeding program, with sustainable and smart Brassica production in a metal-toxic environment.

Proteomic Analysis of the Protective Effect of Eriodictyol on Benzo(a)pyrene-Induced Caco-2 Cytotoxicity

We evaluated the possible protective effects of six polyphenols on benzo(a)pyrene (BaP)-induced cytotoxicity in Caco-2 cells. We show that treatment with quinic acid, ferulic acid, homovanillic acid, trolox and BaP decreased cell viability, whereas naringenin and eriodictyol affected viability in a bi-phasic manner with low concentrations decreasing viability whereas higher concentrations increase viability. Co-treatment with 20 μM eriodictyol or naringenin reduced BaP-induced cytotoxicity, including cell apoptosis, cell cycle progression, and oxidative stress. Our results show that the protective effect of eriodictyol was superior to that of naringenin. The potential protective mechanisms of eriodictyol on BaP-induced toxicity were investigated by proteomics. We identified 80 differentially expressed proteins (DEPs) with proteins associated with genetic information processing pathway representing the highest proportion and number of proteins responding to eriodictyol treatment, including key proteins such as RPA2, SNRPA, RAD23B, NUP155 and AARS. Our results provide new knowledge on how polyphenols may prevent BaP-induced carcinogenesis.

Label-free quantitative proteomics analysis of jujube (Ziziphus jujuba Mill.) during different growth stages

Chinese jujube (Zizyphus jujuba Mill.), a member of the Rhamnaceae family with favorable nutritional and flavor quality, exhibited characteristic climacteric changes during its fruit growth stage. Therefore, fruit samples were harvested at four developmental stages on days 55 (young fruits), 76 (white-mature fruits), 96 (half-red fruits), and 116 (full-red fruits) after flowering (DAF). This study then investigated those four growth stage changes of the jujube proteome using label-free quantification proteomics. The results identified 4762 proteins in the samples, of which 3757 proteins were quantified. Compared with former stages, the stages examined were designated as "76 vs. 55 DAF" group, "96 vs. 76 DAF" group, and "116 vs. 96 DAF" group. Gene Ontology (GO) and KEGG annotation and enrichment analysis of the differentially expressed proteins (DEPs) showed that 76 vs. 55 DAF group pathways represented amino sugar, nucleotide sugar, ascorbate, and aldarate metabolic pathways. These pathways were associated with cell division and resistance. In the study, the jujube fruit puffing slowed down and attained a stable growth stage in the 76 vs. 55 DAF group. However, fatty acid biosynthesis and phenylalanine metabolism was mainly enriched in the 96 vs. 76 DAF group. Fatty acids are precursors of aromatic substances and fat-soluble pigments in fruit. The upregulation of differential proteins at this stage indicates that aromatic compounds were synthesized in large quantities at this stage and that fruit would enter the ripening stage. During the ripening stage, 55 DEPs were identified to be involved in photosynthesis and flavonoid biosynthesis in the 116 vs. 96 DAF group. Also, the fruit entered the mature stage, which showed that flavonoids were produced in large quantities. Furthermore, the color of jujube turned red, and photosynthesis was significantly reduced. Hence, a link was established between protein profiles and growth phenotypes, which will help improve our understanding of jujube fruit growth at the proteomic level.

Proteome Changes Reveal the Protective Roles of Exogenous Citric Acid in Alleviating Cu Toxicity in Brassica napus L

Citric acid (CA), as an organic chelator, plays a vital role in alleviating copper (Cu) stress-mediated oxidative damage, wherein a number of molecular mechanisms alter in plants. However, it remains largely unknown how CA regulates differentially abundant proteins (DAPs) in response to Cu stress in Brassica napus L. In the present study, we aimed to investigate the proteome changes in the leaves of B. L. seedlings in response to CA-mediated alleviation of Cu stress. Exposure of 21-day-old seedlings to Cu (25 and 50 μM) and CA (1.0 mM) for 7 days exhibited a dramatic inhibition of overall growth and considerable increase in the enzymatic activities (POD, SOD, CAT). Using a label-free proteome approach, a total of 6345 proteins were identified in differentially treated leaves, from which 426 proteins were differentially expressed among the treatment groups. Gene ontology (GO) and KEGG pathways analysis revealed that most of the differential abundance proteins were found to be involved in energy and carbohydrate metabolism, photosynthesis, protein metabolism, stress and defense, metal detoxification, and cell wall reorganization. Our results suggest that the downregulation of chlorophyll biosynthetic proteins involved in photosynthesis were consistent with reduced chlorophyll content. The increased abundance of proteins involved in stress and defense indicates that these DAPs might provide significant insights into the adaptation of Brassica seedlings to Cu stress. The abundances of key proteins were further verified by monitoring the mRNA expression level of the respective transcripts. Taken together, these findings provide a potential molecular mechanism towards Cu stress tolerance and open a new route in accelerating the phytoextraction of Cu through exogenous application of CA in B. napus.

Comparative effects of ascobin and glutathione on copper homeostasis and oxidative stress metabolism in mitigation of copper toxicity in rice

Copper (Cu) pollution of agricultural land is a major threat to crop production. Exogenous chemical treatment is an easily accessible and rapid approach to remediate metal toxicity, including Cu toxicity in plants. We compared the effects of ascobin (ASC; ascorbic acid:citric acid at 2:1) and glutathione (GSH) in mitigation of Cu toxicity in rice. Plants subjected to Cu stress displayed growth inhibition and biomass reduction, which were connected to reduced levels of chlorophylls, RWC, total phenolic compounds, carotenoids and Mg²⁺ . Increased accumulation of ROS and malondialdehyde indicated oxidative stress in Cu-stressed plants. However, application of ASC or GSH minimized the inhibitory effects of Cu stress on rice plants by restricting Cu²⁺ uptake and improving mineral balance, chlorophyll content and RWC. Both ASC and GSH pretreatments reduced levels of ROS and malondialdehyde and improved activities of antioxidant enzymes, suggesting their roles in alleviating oxidative damage. A comparison on the effects of ASC and GSH under Cu stress revealed that ASC was more effective in restricting Cu²⁺ accumulation (69.5% by ASC and 57.1% by GSH), Ca²⁺ and Mg²⁺ homeostasis, protection of photosynthetic pigments and activation of antioxidant defence mechanisms [catalase (110.4%), ascorbate peroxidase (76.5%) and guaiacol peroxidase (39.0%) by ASC, and catalase (58.9%) and ascorbate peroxidase (59.9%) by GSH] in rice than GSH, eventually resulting in better protection of ASC-pretreated plants against Cu stress. In conclusion, although ASC and GSH differed in induction of stress protective mechanisms, both were effective in improving rice performance in response to Cu phytotoxicity.

Excess Copper-Induced Alterations of Protein Profiles and Related Physiological Parameters in Citrus Leaves

This present study examined excess copper (Cu) effects on seedling growth, leaf Cu concentration, gas exchange, and protein profiles identified by a two-dimensional electrophoresis (2-DE) based mass spectrometry (MS) approach after Citrus sinensis and Citrus grandis seedlings were treated for six months with 0.5 (control), 200, 300, or 400 μM CuCl2. Forty-one and 37 differentially abundant protein (DAP) spots were identified in Cu-treated C. grandis and C. sinensis leaves, respectively, including some novel DAPs that were not reported in leaves and/or roots. Most of these DAPs were identified only in C. grandis or C. sinensis leaves. More DAPs increased in abundances than DAPs decreased in abundances were observed in Cu-treated C. grandis leaves, but the opposite was true in Cu-treated C. sinensis leaves. Over 50% of DAPs were associated with photosynthesis, carbohydrate, and energy metabolism. Cu-toxicity-induced reduction in leaf CO2 assimilation might be caused by decreased abundances of proteins related to photosynthetic electron transport chain (PETC) and CO2 assimilation. Cu-effects on PETC were more pronounced in C. sinensis leaves than in C. grandis leaves. DAPs related to antioxidation and detoxification, protein folding and assembly (viz., chaperones and folding catalysts), and signal transduction might be involved in Citrus Cu-toxicity and Cu-tolerance.

Morpho-Physiological and Proteomic Analyses of Eucalyptus camaldulensis as a Bioremediator in Copper-Polluted Soil in Saudi Arabia

The present investigation aimed to assess the impact of copper (Cu) stress on the physiological and proteomic behavior of Eucalyptus camaldulensis.E. camaldulensis is likely a potential phytoremediator in areas vulnerable to Cu contamination, such as the industrial areas of Riyadh. To realize this objective, young seedlings of E. camaldulensis were potted in an open area with soil comprised of clay and sand. Different doses of Cu (30, 50, and 100 µM) were applied to the plants as CuSO₄·5H₂O for 6 weeks. Plant growth was monitored during the Cu exposure period, and morphological and physiological indicators were measured once a week to determine the growth rates. A proteomics study was also conducted to find out the influence of Cu stress on proteins. Our results showed that growth was negatively affected by Cu treatment, particularly at the highest concentrations. Moreover, using a proteomic analysis showed 26 targets involved in protein expression. Elevated levels of Cu increased the expression of 11 proteins and decreased the expression of 15 proteins. Changes were detected in proteins involved in photosynthesis, translation, transcription, metabolism, and antioxidant enzymes. Our findings provided insights into the molecular mechanisms related to Cu stress, in addition to its influence on the morphological and physiological attributes of E. camaldulensis seedlings. This investigation aimed to characterize the mechanism behind the impact of Cu stress on the plant.

Influence of Heavy Metals (Ni, Cu, and Zn) on Nitro-Oxidative Stress Responses, Proteome Regulation and Allergen Production in Basil (Ocimum basilicum L.) Plants

One of the most significant biosphere contamination problems worldwide is derived from heavy metals. Heavy metals can be highly reactive and toxic according to their oxidation levels. Their toxic effects are associated with the increased production of reactive oxygen species (ROS) and cellular damage induced in plants. The present study focuses on the effects of nickel (Ni), copper (Cu), and zinc (Zn) applied to the soil on the antioxidant response and allergen production in the aromatic plant basil (Ocimum basilicum L.) following a combined physiological, biochemical and analytical approach. The concentrations used for the three heavy metals were based on the 2002 Regulation of the Polish Ministry of the Environment on Soil Quality Standards [(i) agricultural land (group B): Ni 100 ppm, Ni 210 ppm, Cu 200 ppm, Cu 500 ppm, Zn 720 ppm and (ii) industrial land (group C): Ni 500 ppm, Cu 1000 ppm, Zn 1500 ppm, Zn 3000 ppm]. The highest physiological and cellular damage in basil plants was caused by Cu and Zn. Increasing concentrations of Cu resulted in a further increase in cellular damage and nitro-oxidative stress, correlating with an induction in activity of reactive oxygen and nitrogen species metabolism enzymes (SOD, CAT, APX, NR). Treatment with Cu led to increased concentration of the allergenic protein profilin, while increasing concentrations of Cu and Zn led to a decrease in the concentration of total proteins (likely due to proteolysis) and antioxidant capacity. Interestingly, severe Cu stress resulted in the accumulation of specific proteins related to transpiration and photosynthetic processes. On the basis of these findings, Ni stress in basil plants appears to be less damaging and with lower allergenic potential compared with Cu and Zn stress, while Cu-stressed basil plants experience most detrimental effects and display highest allergen production.