Salinity poses a significant challenge to sustainable agriculture by disrupting plant growth and development. It primarily exerts its negative effects by extracting water from the cytoplasm, leading to osmotic stress (Akula and Ravishankar, 2011). Osmotic stress disrupts metabolic balance and leads to the accumulation of harmful reactive oxygen species (ROS), exacerbating cellular damage and impairing plant function (Younessi-Hamzekhanlu et al., 2021; Zhao et al., 2021), induces specific secondary metabolites production, stimulates the activity of ROS scavenging enzymes (Huang et al., 2020), and affects photosynthesis through destabilizing the chloroplast structure, chlorophyll biosynthesis, and eventually photosynthetic rate (Hnilickova et al., 2021). Plants respond to salinity by modulating various morphological, physiological, and biochemical traits by regulating ion homeostasis and biosynthesis of osmoprotectants, antioxidants, and phytohormones (Arif et al., 2020). Utilization of the impressive proteomics technologies could provide noteworthy information about the complex impact of stress on medicinal plants along with stress-tolerance mechanisms concerning photosynthesis, ion homeostasis, ROS signaling, protein phosphorylation, osmotic modulation, signaling transduction, and post-translational regulation (Zhang et al., 2023).

In general terms, it is believed that the process of photosynthesis is sensitive to salinity. Up-regulation of Rubisco activase, Rubisco large subunit, and carbonic anhydrase as photosynthetic proteins was observed in the proteomic response of medicinal halophyte Limonium bicolor (bicolored sea lavender) leaves under salt stress. The elevated abundance of these proteins, which boosted photosynthesis levels, played a crucial role in enabling Limonium bicolor to withstand salt stress (Wang et al., 2017). In Aeluropus lagopoides, salt stress led to the downregulation of Rubisco’s small subunit at the protein level (Sobhanian et al., 2010). Similar results have also been reported in association with photosynthetic proteins including Rubisco small subunit, LOC100194054, Cytb6-f, oxygen-evolving enhancer with differential accumulation patterns in response to salt stress in Imperata cylindrica (L.) medicinal plant (Shih YunJhih et al., 2018). With a focus on the effect of salt stress on proteins of chloroplasts in Amaranthus cruentus as a photosynthetic C3-C4 medicinal plant by LC-MS/MS, Joaquín-Ramos et al. (2014) also reported that salt stress triggered alterations in the proteomic profiles of thylakoid protein complexes in both bundle sheath cells and mesophyll cells were induced by salt stress; in addition, enhancement of ATP-synthase and the CYTb6f proteins were associated with a significant demand for ATP during the salt stress response.

High ATP utilization in the leaves of Morus alba L. under salt stress resulted in an increased NADPH/ATP ratio, thereby enhancing cyclic electron flow (CEF) (Huihui et al., 2020). Reduced ATP synthesis plays a role in minimizing photoinhibition (Takagi et al., 2017). TMT-based proteomics analysis revealed that mulberry seedlings exposed to NaCl and NaHCO₃ stress exhibited disruptions in internal photoprotective mechanisms. The down-regulated xanthophyll cycle, cyclic electron flow (CEF), chlorophyll synthesis, Fd-dependent ROS metabolism and nitrogen metabolism due to decrease in abundance of the LHCII antenna (CP24 10A, CP26, and CP29), PSII oxygen-evolving complex (OEE3–1 and PPD4), and photosystem I core proteins (PsaF, PsaG, PsaH, PsaN, Ycf4) inhibited photosystem electron transfer and carbon assimilation. Therefore, the main prerequisite to keeping plants’ photosynthetic function and improving plant tolerance under stress conditions was photoinhibition as an effective regulatory mechanism (Huihui et al., 2020).

Plants activate diverse mechanisms to counteract salinity, including the stimulation of protective and antioxidant enzymes. A systematic proteomic analysis of Andrographis paniculata under salinity stress, employing a combination of 2-DE and MS, identified proteins that were upregulated and downregulated in response to stress. These proteins, which contributed to stress protection, were associated with superoxide dismutase, ascorbate peroxidase, and ribulose-1,5-bisphosphate oxygenase, functioning as ROS scavengers (Talei et al., 2015). It was suggested that Limonium bicolor leaves high stress-tolerance was due to its great constitutive antioxidant and detoxification capacity (Wang et al., 2017).

The root proteome profiling of Pongamia pinnata under salt stress was performed by employing the free-labeled nanoLC-MS/MS method, showing an elevated presence of proteins associated with essential regulatory pathways, including chalcone synthase (CHS) proteins, which take part in flavonoid biosynthesis, were involved in signaling pathways, including secondary metabolism, anaerobic respiration, and antioxidant metabolism associated with salt tolerance. Moreover, the significant abundance of CHS proteins has contributed to adjusting ROS cellular energy redox homeostasis against Na⁺ toxicity with high antioxidant activity under saline environment conditions (Marriboina et al., 2022).

Plants activate a series of responses and defense mechanisms facing abiotic stresses to transmit signals and increase tolerance ( Table 3 ). The comparative proteomic analyses of Limonium bicolor leaf and root exposed to salt stress utilizing 2D-PAGE combined with MALDI-TOF/TOF-MS revealed DAPs with diverse physiological functions spanning a broad spectrum of molecular processes leading to salt-stress adaptation and some chemical constituent enhancement by activating multiple biological pathways including energy, secondary metabolism, redox homeostasis, carbohydrate, transcription, and transport (Wang et al., 2017). iTRAQ-labeled quantitative proteomics in Helianthus tuberosus L. under salt stress revealed that DAPs were predominantly enhanced in redox regulation, carbohydrate metabolism, ion binding processes, and ribosome translation (Zhang et al., 2018). A rise in soluble carbohydrates, restructuring of ribosomes, and elevated levels of enzymes participating in the citrate cycle, glycolysis, and the pentose phosphate pathway, with an impact on plant developmental processes and controlling organelle trafficking energy resource could conduct modulation of the plant metabolism in salt defense (Li et al., 2015). Hence, the induction of sugar signaling proteins and ribosome activity was introduced as the reason for the salt tolerance appearance in H. tuberosus (Zhang et al., 2018). The utilization of (iTRAQ) MS/MS by Liu Z. et al. (2019) significantly enabled the detection of the changes in proteins and related molecular mechanisms in Spica prunellae, a Chinese traditional herb under different salt concentrations. Salt-stressed Spica prunellae activated a bunch of mechanisms by enhancing proteins related to energy metabolism, protein metabolism, photosynthesis, and oxidative capacity that afford tolerance to salt stress.

Light is a critical environmental factor influencing plant growth and development. The balance between photoreception and intensity directly impacts photosynthetic efficiency. Under natural conditions, plants often receive suboptimal light, resulting in photosynthetic imbalance. Both excessive and insufficient light can damage protein complexes involved in electron transport, disrupting NADPH and ATP availability. To adapt to these stresses, photosynthetic organisms employ various photoprotective mechanisms and protein modifications. Thylakoid membrane protein complexes, such as photosystems (PS) I and II, their light-harvesting antennae (LHC I and II), cytochrome (Cyt) b6f, and the ATP-synthase complex, work in coordination to absorb light energy and convert it into a chemical form essential for plant survival (Wietrzynski et al., 2020). Protection mechanisms have evolved in PSII to counteract ROS generation by tuning redox processes and inhibiting damage to the photosystem (Brinkert et al., 2016). Ultraviolet (UV) radiation is the most impressive ray of light that impacts every level of plants’ biological organization and alters the biochemistry of plants. Ultraviolet radiation activates the photoregulatory pathway (Brown and Jenkins, 2008), damages photosynthetic pigments (Frohnmeyer and Staiger, 2003), enhances ROS production (Trentin et al., 2015), and elicits secondary metabolite production in medicinal plants (Binder et al., 2009). The impact of light or UV radiation on particular biological pathways and processes can be described by alterations in the contents of proteins that have a functional role in the performance of photosynthesis.

Plants activate defense strategies by regulating specific genes and accumulating UV-absorbing compounds in response to light/UV stress (Frohnmeyer and Staiger, 2003). Modern pharmacological studies have confirmed the high medicinal value of Lonicera japonica. The main molecular processes involved in its development when exposed to UV radiation were analyzed by comparative proteomics. Studies have shown that UV radiation significantly increases the levels of proteins involved in antioxidant activity, energy and carbohydrate metabolism, and secondary metabolite content in Lonicera japonica flower buds. These alterations in bioactive components, primarily secondary metabolites, influence both the quality and quantity of the resulting medicinal materials (Zhu et al., 2017). Similar results have also been reported in association with the effect of blue/red light on Scrophularia kakudensis proteomic profiles, referring to up-regulation of carbohydrate metabolism, photosynthesis, and stress responses as well as stimulation of secondary metabolites with medicinal value via activated stress alleviation mechanisms (Manivannan et al., 2021). Comparative proteomics using 2-DE combined with MALDI-TOF/TOF MS was conducted to identify key enzymes involved in metabolite biosynthesis and defense mechanisms in UV-irradiated Lonicera japonica. Findings suggested that UV stress activated a complex defense system, leading to differential protein accumulation across various molecular processes, including photosynthesis, secondary metabolite biosynthesis, transport, carbohydrate and energy metabolism, cell wall dynamics, and lipid metabolism. Enhanced levels of caffeoylquinic acids and iridoids were recognized as secondary metabolites with antioxidant and UV-absorbing properties. Additionally, an increase in DXR (one-deoxy-D-xylulose 5-phosphate reductoisomerase) and EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) production, as two UV-responsive key enzymes, provides more precursors for secondary metabolite biosynthetic pathways following exposure to UV stress (Zhang et al., 2013).

High radiation may disrupt the balance between the energy absorbed through the photophysical processes of PSII and the energy utilized for carbon assimilation (Joshi et al., 2011). The major function of chloroplasts, namely photosynthesis, could be severely suppressed by enhanced UV-B irradiation. To prevent UV-B’s detrimental effects on photosynthesis, flavonoids are actively expressed, acting both as an internal filter against this harmful radiation and participating in the antioxidant defense system (Ferreyra et al., 2021). Zhu et al. (2015) also discussed the negative impact of UV-B irradiation and dark incubation on photosynthesis in Catharanthus roseus leaves by reporting the diminution in abundance of sedoheptulose-1, 7-bisphosphatase, chlorophyll a/b binding protein, serine glyoxylate aminotransferase 3, ribulose bisphosphate carboxylase/oxygenase, and light-harvesting complex II proteins. The declining production of RuBisCO and PSII-related proteins, in both whole leaves and chloroplasts, implies the adverse effect of UV-B irradiation on the photosynthetic system efficiency. Obtained data from a comparative proteomic approach confirmed that augmented UV-B radiation exposure up-regulated antioxidant, stress-responsive proteins, and flavonoid biosynthesis enzymes, while reducing photosynthesis rate in Ginkgo biloba traditional medicinal plant (Zheng et al., 2015). Catharanthus roseus synthesizes a diverse range of indole alkaloids, which exhibit notable pharmaceutical properties. Comparative gel-free proteomics revealed a high abundance of 10-hydroxy geraniol oxidoreductase, involved in the biosynthesis of indole alkaloids in C. roseus leaves. The UV-B irradiation and darkness induced alkaloid biosynthesis by altering related metabolic pathways and therewith significantly boosted indole alkaloids, including ajmalicine, vindoline, catharanthine, and strictosidine production (Zhu et al., 2015). UV-B radiation could have a remarkable positive effect on the medicinally active substances, namely rotenoids, flavonoids, and coumarins, as the secondary metabolite. To focus on the role of UV-B radiation in regulating the metabolism of M. himalaica, a Tibetan medicinal plant, an iTRAQ proteomics approach was used. It was found that under exposure to UV-B radiation, up-regulation of DAPs such as the chalcone synthase enzymes improved the biosynthesis of rotenoid through the hormone signaling systems and phosphatidylinositol, including auxin, abscisic acid, jasmonic acid, and calcium signals (Gu et al., 2018). Mitochondrial proteomics was employed to investigate the response mechanism of Clematis terniflora, a medicinal plant from the Ranunculaceae family, to UV-B radiation and dark treatment. DAPs were primarily linked to mitochondrial membrane permeability, the mitochondrial electron transport chain (mETC), photorespiration, and the tricarboxylic acid cycle, to minimize energy consumption and maintain energy balance under stress. Additionally, alternative oxidases played a role in regulating intracellular oxygen balance by engaging other oxygen-consuming pathways (Tao et al., 2022).

Water deficit is one of the most intense environmental restrictions on plant productivity. Drought stress disturbs plant water relations and diminishes water-use efficiency, root proliferation, and eventually yield (Kazemi Oskuei et al., 2023). Drought conditions also affect plants’ metabolic processes and lead to cellular damage (Perlikowski et al., 2022; Sahithi et al., 2021). However, concerning spice and medicinal plants, the situation is different. Drought has a significant effect on the growth and secondary metabolic pathways of medicinal plants. Exposure to drought stress reduces medicinal plants’ biomass production as well, yet enhances the contents and quality of important compounds (Shil and Dewanjee, 2022). Various response strategies in plants have been proposed at physiological and biochemical levels to cope with drought stress (Farooq et al., 2009).

To trigger the defense mechanisms immediately during any stress, various stress-responsive proteins remain active in plants. For the relative protein profiling of chrysanthemum (Dendranthema grandiflorum) Sahithi et al. (2021) performed 2-DEs combined with MALDI-TOF MS. Most of the DAPs under drought stress conditions were mostly related to flower development and stress response/defense. An increase in stress response proteins’ content was associated with reduced reactive oxygen species (ROS) and redox reaction regulation to protect the cell from oxidative damage and maintain homeostasis (Sahithi et al., 2021).

The seeds of Taxillus chinensis, belonging to Taxillus, a genus of parasitic plants that are important herbs in the Chinese pharmaceutical industry, are sensitive to dehydration. Dehydration stress induces oxidative damage in seeds. Proteomics analysis using TMT-labeling and LC-MS/MS identified DAPs primarily localized in the chloroplast, playing key roles in photosynthesis, signal transduction, and energy metabolism. Increased levels of Calvin cycle-associated and glycolysis-related proteins, such as fructose aldolases and glucose pyrophosphorylase, contribute to energy production and enhanced dehydration tolerance in Loranthus seeds (Pan et al., 2022). The up-regulation of chloroplast chaperonins involved in refolding and protein complexes protection, along with the down-regulation of cytochrome b, Rubisco large subunit, the ascorbate peroxidase and oxygen-evolving complexes, as mitochondrial proteins, disclosed the central role of chloroplasts and mitochondria in abiotic stress adaptation in Amaranthus hypochondriacus L (Huerta-Ocampo et al., 2009).

Up-regulation of GA-responsive protein and anthranilate synthase as indoleacetic acids (IAA)-related proteins in leaves of Scutellaria baicalensis, a traditional Chinese herbal plant exposed to water deficit, was detected by proteomic analysis, demonstrating the effect of water deficits on flavonoid accumulation through hormonal metabolism regulation. The great accumulation of flavonoids as active compounds affects the high quality of this herbal medicine (Yuan et al., 2012). In addition, an appropriate degree of drought promotes baicalin accumulation, stimulating the production of key biosynthetic enzymes (L. Cheng et al., 2018). The proteomic profiles of drought-stressed Mulberry Trees (Morus alba L.) showed DAPs mostly enriched in the sucrose-related metabolic pathway (Liu et al., 2019a).

The differential regulation of proteins involved in cell wall strengthening, signal transduction, gene regulation, and cellular detoxification affects the molecular mechanism behind drought stress tolerance (Kottapalli et al., 2009). Proteomic analysis of Lepidium draba under drought stress revealed differential regulation of key proteins involved in energy metabolism and photosynthesis, including rubisco activase A, RuBisCO large subunit, aminomethyl transferase mitochondrial-like proteins, endopeptidase La protein, and oxygen-evolving enhancer protein 1–2 (OEE1-2). Additionally, the two-component system (TCS), comprising histidine kinase proteins (HKs), histidine phosphotransfer proteins (Hpts), and response regulator proteins (RRs), played a role in signal transduction and environmental sensing. Glycosyltransferase contributed to plant development, while glutamate 5-kinase, a component of the proline biosynthesis pathway, likely enhanced drought tolerance in L. draba (Jamshidi Goharrizi et al., 2020). Comparative proteomics of chrysanthemum leaves under drought stress identified DAPs involved in flower development, stress signaling pathways, and secondary metabolic processes, including the regulation of the circadian rhythm, physiological transport, DNA synthesis, gene expression, and protein ubiquitination. These findings contributed to defining the key signaling networks, homeostatic regulation, and tolerance mechanisms, essential for chrysanthemum’s adaptation to drought stress (Sahithi et al., 2021). In the view of Jaffar et al. (2016), the overaccumulation of CmWRKY10, which is known as DNA DNA-binding protein in chrysanthemum, was induced by drought to behave as a positive regulator of stress-related genes with a role in ABA signaling and cellular ROS production, and improve its drought tolerance. Receptor-like cytosolic kinases CLE25 contribute to transmitting drought signals to downstream targets, leading to the activation of NCED3, a crucial enzyme in abscisic acid (ABA) biosynthesis (Takahashi et al., 2018). Therefore, the involvement of protein kinases in stress signal transduction is co-regulated with plant responses to drought stress in all aspects.

Temperature is one of the most critical abiotic stresses that profoundly affects plant growth and productivity (Parankusam et al., 2017). Both heat stress (high temperatures) and cold stress (low temperatures) significantly disrupt the physiological processes of plants, including protein synthesis, metabolism, and cellular integrity. Each medicinal plant species has its own optimal temperature range; extreme variations can quickly disrupt its cellular structures, macromolecules, and, in particular, valuable secondary metabolites (Alum, 2025). Hence, medicinal plants similar to crops have evolved different adaptation mechanisms to withstand adverse conditions for optimal growth (Niu and Xiang, 2018). The induction of variety cellular phenomena, namely membrane fluidity, metabolite, osmolyte concentrations, photosynthesis, carbon assimilation, and redox status, constitutes responses to heat stress (Niu and Xiang, 2018). According to the Sher et al. (2024) the alteration of the post-translational, transcriptional, and translational mechanisms, followed by changes in signaling pathways, is a key strategy for combating heat stress in medicinal plants. High or low temperatures disrupt protein stability, specific enzyme functions, and perturb metabolism. Therefore, the identification of protein profiles of medicinal plants by proteomics in response to extreme temperatures is crucial to understand the molecular mechanisms that underpin response strategies in medicinal plants’.

The heat shock transcription factors (HsfA1s), which are the master regulators of the heat stress response (HSR), acquire thermotolerance in plants through interaction with heat shock proteins (HSPs). So, the enhancement in the level of HsfA1s and HSPs (HSP70 and HSP90) leads to adaptation and heat stress tolerance in medicinal plants (Ohama et al., 2016). Gouda et al. (2024) reported that the optimal response in which cells survive the heat stress was the elevation of HSP levels as heat-responsive proteins. In addition, the upregulation of HSPs prevented other cellular proteins from damage caused by heat stress.

The evaluation of heat-responsive proteins in P. ternata through 2-DE followed by MALDI-TOF/TOF MS showed that in the protein expression pattern, more than 20 proteins were up- and down-regulated in response to heat stress. Several tolerance-related proteins with various functions were identified, including small HSPs, RNA processing proteins, photosynthesis proteins, protein degradation proteins, and defense proteins (Zhu et al., 2013). It was reported that heat stress reduced the photosynthetic efficiency of Ginseng (Panax ginseng Meyer) 48 h after treatment, and modulated 847 differentially abundant proteins, which were identified by label-free quantitative proteome analysis in response to stress. These proteins with increased abundance were mainly associated with antioxidant and translation-regulating activities, whereas the proteins related to the receptor chaperones, G-proteins, calcium-signaling proteins, transcription factors, structural-binding, and transfer/carrier proteins activities exhibited reduced abundance (Kim et al., 2019). DAPs in the leaves of Dendranthema grandiflorum ‘Jinba’ under high temperature stress were investigated using label-free quantitative proteomics techniques and LC-MS/M. It was demonstrated that most of the DAPs were involved in energy metabolism pathways, protein metabolism, and heat shock, as well as some of them had a correlation with heat resistance in chrysanthemum (Li et al., 2021b). Proteomic analysis of Maca (Lepidium meyenii Walp) showed that the levels of 300 proteins, in particular, HSP proteins, which regulate protein quality, were differentially changed in response to the high temperature stress. HSPs were significantly up-regulated to protect other proteins from being denatured. Moreover, a variety of transcription factors, including MBF1C, HSFA2, AF1, WRKY70, and HY5, that take part in the inspection of HSR-related genes, ROS scavengers, and enzymes, were regulated by these HSPs (Wang et al., 2020).

Likewise, proteomic analyses revealed that cold acclimation enhanced the cold tolerance of medicinal plants by promoting the biosynthesis of proteins that participated in ROS scavenging, photosynthesis, energy metabolism, carbohydrate metabolism, protein metabolism, and cofactor biosynthesis (Dugganaboyana et al., 2023). By using MALDI-TOF/TOF-MS, Shen et al. (2021) found some proteins in G8, such as TIM, ATPB, and LEA in both cold-acclimated and non-acclimated S. apetala seedlings, which act as common responsive proteins in response to chilling stress. Also, they suggested that CAB, eEF-G and APX1 proteins function as the hub proteins in regulating the stress response. Zhang et al. (2023), using integrated transcriptomics (RNA-seq) and proteomics (iTRAQ) techniques, have revealed the enrichment of some pathways comprising antioxidant activity and carbohydrate metabolism through the induction of six different genes (GLUST, GO1, RPE3, P5PI3, RbcS, and POD4) and differentially expressed two heat shock proteins (Hsp18 and Hsp70) in two CfT lines of (cold-resistant) R. chrysanthum exposed to cold stress. Comparative proteomics of Ammopiptanthus mongolicus leaves under cold stress identified differentially accumulated proteins involved in photosynthesis in chloroplasts, reactive oxygen species scavenging, defense system, protein synthesis, protein folding, and protein degradation (Zheng et al., 2023). The findings of Pan et al. (2025) revealed that the differentially expressed proteins were predominantly involved in biosynthesis, transport, energy, and cellular metabolism in T. chinensis seeds under chilling stress. There was an investigation of the cold stress tolerance mechanism in Calendula officinalis, assessing 2-DE and MALDI-TOF-MS proteomic analyses in exposure to 4 °C at different time intervals. It was indicated that Calendula officinalis, which is an important medicinal plant, can withstand cold stress due to the involvement of proteins corresponding to photosynthesis, respiration, stress resistance, antioxidant defense, plant development, and signal transduction. Furthermore, the main pathway for protecting this plant against cold stress were introduced as the Glutathione-ascorbate pathway and different antioxidants (Jan et al., 2023).

One of the major abiotic stresses that leads to serious effects in plants is heavy metal (HM) toxicity. Heavy metal (HM) term is generally used for an extensive range of metal(loid)s that are natural constituents of soils including nickel (Ni), cobalt (Co), cadmium (Cd), copper (Cu), chromium (Cr), lead (Pb), zinc (Zn), boron(B), and arsenic (As); the presence of these toxic ions seriously alters the physiological and metabolic processes of living organisms. However, most of the heavy metal(loid)s are indeed micronutrients and/or elements essential in small quantities for the functional behaviors of many proteins associated with supporting the normal growth and development of plants (Alloway, 2013). Generally, an extensive consequence of HM ions’ entrance into cells is interacting with vital constituents, inactivating the enzymes, interacting with sulfhydryl groups of proteins, displacement of essential cations from their specific binding sites, and excessive ROS generation contribute to oxidative damage in lipids, nucleic acids, and proteins, and ultimately inhibiting plant growth and causing cell death (Hossain et al., 2012).

To withstand excess HMs, plants use diverse strategies as coordinated homeostatic mechanisms leading to uptake limitation or sequestration, as well as constitutive and adaptive mechanisms.

The compatible solutes, metallothionein, phytochelatins, and secondary metabolites are part of various molecules that participate in attenuating the negative impact of HMs. Hence, gaining information at the translational and/or post-translational levels, and identifying the function of genes/proteins, are fundamental steps in understanding the molecular mechanisms of heavy-metal stress responses and developing tolerant transgenic plants that are capable of detoxification or toxic elements removal from soils (Riyazuddin et al., 2021). Comparative or quantitative proteomics studies represent an efficient platform for the recognition of biologically functional complex protein networks in organisms subjected to constraints. Proteomics provides a preferable concept of the specific mechanisms and biochemical pathways related to tolerance mechanisms to metal stress and cellular detoxification (Hossain and Komatsu, 2013).

Certainly, limited research has been performed on the effects of heavy-metal stress on pharmacologically active substances and the protein abundance of medical plants in the last decades ( Table 3 ). Cannabis sativa, which is an important, tolerant herbaceous species from central Asia, has a high capability to cope with high metal concentrations in soil. The proteomic analysis of Cannabis sativa roots exposed to high Copper concentration (Bona et al., 2007) exhibited that the Copper treatment up-regulated putative auxin-induced proteins such as plant growth regulator-related proteins, formate dehydrogenase (FDH), which plays a role in maintaining a reduced environment, and the scavenging system proteins represented by aldo/keto reductase. While stress-responsive proteins enolase and elicitor inducible stress resistance proteins cyclophilin and putative peroxidase, and suitable growth regulator proteins glycine-rich RNA binding protein (GRP) were down-regulated.

The high accumulation of HMs inhibited the plant’s growth and its photosynthetic product. The separation of proteins from Agrostis capillaris L. under metal stress with 2-DE and identification by LC-MS/MS demonstrated that high Copper concentration severely disrupted the photosynthesis apparatus and impacted both light-dependent and -independent photosynthetic pathway-related proteins like cytochrome b6-f complex, oxygen-evolving enhancer protein 1 (OEE), chlorophyll a-b binding proteins, and RuBisCO. The enhancement of redox enzymes, isocitrate dehydrogenase, cysteine/methionine synthases, and chaperones in Agrostis capillaris L. was related to Cu detoxification and tolerance of this metallicolous plant (Hego et al., 2016).

Alotaibi et al. (2019) characterized the molecular mechanism underlying the impact of Cu stress on Eucalyptus camaldulensis and the achievement of homeostasis in response to this metal. As attested by the proteomics results, altered proteins were involved in photosynthesis, protein metabolism, and regulation; special stress-related proteins further assisted E. camaldulensis seedlings in handling Cu exposure. Comparative proteomic analysis of Hyoscyamus albus L. seedlings exposed to copper revealed that proteins involved in proteasome were decreased in abundance whilst the energy supply and anabolism proteins were increased as well as newly generated proteins acting as Cu-binding reservoirs for deposition of additional Cu. It was indicated that high levels of Cu increased the activity of respiration and promoted the propagation of H. albus roots by enhancing proteins associated with protein synthesis, carbohydrate metabolism, and ATP synthesis (Sako et al., 2016).

According to proteomic analysis, arsenic bioaccumulation negatively impacted most of the proteins related to energy and carbon metabolism inducing a metabolic disorder in the Acacia farnesiana (Sweet Acacia) medicinal plant utilized in Mexican traditional medicine. Since Acacia farnesiana under Arsenic stress requires more energy to maintain cellular homeostasis, endosymbiosis with Methylobacterium sp. provided the required energy to cope with arsenic through up-regulation of carbonic anhydrase which promotes the photosynthetic activity. In addition, the up-regulated defense-related proteins were involved directly in the ASC-GSH cycle and ROS metabolism (Alcántara-Martínez et al., 2018). The substantial amounts of secondary metabolites in Tetraena qatarensis indicated its potential medicinal significance. MALDI-TOF/MS and in silico proteome analysis of lead-treated Tetraena qatarensis demonstrated DAPs having a role in ion and protein binding, transport, antioxidant activity, and abiotic stress response. In spite of the increased level of proteins linked with HSF1-mediated heat shock proteins regulation, glutathione metabolism, and cellular response as stress-regulating metabolic pathways, the role of the identified proteins, in particular, up-regulated glycine-rich protein (GRP) in Pb tolerance and or detoxification has not been clarified (Usman et al., 2022). Analysis of Cd-exposed soybean samples by 2-DE coupled with MS revealed DAPs associated with Cd-chelating pathways. Moreover, increased xylem lignification prevented translocation of Cd from the roots to the aerial parts by significantly up-regulation of lignin biosynthesis-associated proteins under Cd stress (Ahsan et al., 2012). Jin et al. (2016) submitted a report regarding higher Cd enrichment in Amaranthus hybridus L. roots in comparison with other organs as well as the identified DAPs by MALDI-TOF MS indicated that the redirection of root cell metabolism was the main survival mechanism of A. hybridus under Cd stress. Moreover, it was proven that tolerance and enrichment strategies were activated in A. hybridus through up-regulation of proteins related to protein metabolism (proteasome subunit alpha type and ClpC protease), energy metabolism (fructokinase, ATP synthase subunit beta, 2-phospho-D-glyceratehydrolase, enolase, and fructose-biphosphatealdolase), stress and defense (salt tolerance protein I, GST, and salt tolerance protein II) and signal transduction (wall-associated receptor kinase-like14 and phytochrome C) to tolerate Cd stress.