Proteomic analysis of flooded soybean root exposed to aluminum oxide nanoparticles

Nanoparticles as a Tool for Alleviating Plant Stress: Mechanisms, Implications, and Challenges

Plants, being sessile, are continuously exposed to varietal environmental stressors, which consequently induce various bio-physiological changes in plants that hinder their growth and development. Oxidative stress is one of the undesirable consequences in plants triggered due to imbalance in their antioxidant defense system. Biochemical studies suggest that nanoparticles are known to affect the antioxidant system, photosynthesis, and DNA expression in plants. In addition, they are known to boost the capacity of antioxidant systems, thereby contributing to the tolerance of plants to oxidative stress. This review study attempts to present the overview of the role of nanoparticles in plant growth and development, especially emphasizing their role as antioxidants. Furthermore, the review delves into the intricate connections between nanoparticles and plant signaling pathways, highlighting their influence on gene expression and stress-responsive mechanisms. Finally, the implications of nanoparticle-assisted antioxidant strategies in sustainable agriculture, considering their potential to enhance crop yield, stress tolerance, and overall plant resilience, are discussed.

Nano-elicitation and hydroponics: a synergism to enhance plant productivity and secondary metabolism

MAIN CONCLUSION

This review has explored the importance of using a synergistic approach of nano-elicitation and hydroponics to improve plant growth and metabolite production. Furthermore, it emphasizes the significance of green nanotechnology and eco-friendly practices while utilizing this approach to promote the development of a sustainable agriculture system. Nano-elicitation stimulates metabolic processes in plants using nanoparticles (NPs) as elicitors. The stimulation of these biochemical processes can enhance plant yield and productivity, along with the production of secondary metabolites. Nanoparticles have garnered the attention of scientific community because of their unique characteristics, such as incredibly small size and large surface-to-volume ratio, which make them effective elicitors. Hydroponic systems, which optimize growing conditions to increase plant production, are typically used to study the effect of elicitors. By integrating these two approaches, the qualitative and quantitative output of plants can be increased while employing minimal resources. As the global demand for high-quality crops and bioactive compounds surges, embracing this synergistic approach alongside sustainable farming practices can pave the way for resilient agricultural systems, ensuring food security and fostering an eco-friendly environment.

Proteomic insights to decipher nanoparticle uptake, translocation, and intercellular mechanisms in plants

Advent of proteomic techniques has made it possible to identify a broad spectrum of proteins in living systems. Studying the impact of nanoparticle (NP)-mediated plant protein responses is an emerging field. NPs are continuously being released into the environment and directly or indirectly affect plant's biochemistry. Exposure of plants to NPs, especially crops, poses a significant risk to the food chain, leading to changes in underlying metabolic processes. Once absorbed by plants, NPs interact with cellular proteins, thereby inducing changes in plant protein patterns. Based on the reactivity, properties, and translocation of nanoparticles, NPs can interfere with proteins involved in various cellular processes in plants such as energy regulation, redox metabolism, and cytotoxicity. Such interactions of NPs at the subcellular level enhance ROS scavenging activity, especially under stress conditions. Although higher concentrations of NPs induce ROS production and hinder oxidative mechanisms under stress conditions, NPs also mediate metabolic changes from fermentation to normal cellular processes. Although there has been lots of work conducted to understand the different effects of NPs on plants, the knowledge of proteomic responses of plants toward NPs is still very limited. This review has focused on the multi-omic analysis of NP interaction mechanisms with crop plants mainly centering on the proteomic perspective in response to both stress and non-stressed conditions. Furthermore, NP-specific interaction mechanisms with the biological pathways are discussed in detail.

The update and transport of aluminum nanoparticles in plants and their biochemical and molecular phototoxicity on plant growth and development: A systematic review

As aluminum nanoparticles (Al-NPs) are widely used in our daily life and various industries, Al-NPs has been becoming an emerging pollution in the environment. The impact of this NP has been attracting more and more attention from the scientific communities. In this review, we systematically summarized the interactions, uptake, and transport of Al-NPs in the plant system. Al-NPs can enter plants through different pathways and accumulate in various tissues, leading to alter plant growth and development. Al-NPs also affected root, shoot, and leaf characteristics as well as changing nutrient uptake and distribution and inducing oxidative stress via excess reactive radical generation, thereby impairing plant defense systems. Additionally, Al-NPs altered gene expression, which involved in various signaling pathways and metabolic processes in plants, that further altered plants susceptible or tolerant to stressors. The review also emphasized the effects of Al-NP size, surface charge, concentration, and exposure duration on plant growth and development. In the future, more research should be focused on mechanisms underlying Al-NPs phytotoxicity and potential risk to humans and off-target species.

Use of metal nanoparticles in agriculture. A review on the effects on plant germination

Agricultural nanotechnology has become a powerful tool to help crops and improve agricultural production in the context of a growing world population. However, its application can have some problems with the development of harvests, especially during germination. This review evaluates nanoparticles with essential (Cu, Fe, Ni and Zn) and non-essential (Ag and Ti) elements on plant germination. In general, the effect of nanoparticles depends on several factors (dose, treatment time, application method, type of nanoparticle and plant). In addition, pH and ionic strength are relevant when applying nanoparticles to the soil. In the case of essential element nanoparticles, Fe nanoparticles show better results in improving nutrient uptake, improving germination, and the possibility of magnetic properties could favor their use in the removal of pollutants. In the case of Cu and Zn nanoparticles, they can be beneficial at low concentrations, while their excess presents toxicity and negatively affects germination. About nanoparticles of non-essential elements, both Ti and Ag nanoparticles can be helpful for nutrient uptake. However, their potential effects depend highly on the crop type, particle size and concentration. Overall, nanotechnology in agriculture is still in its early stages of development, and more research is needed to understand potential environmental and public health impacts.

Multifactorial role of nanoparticles in alleviating environmental stresses for sustainable crop production and protection

In the era of dire environmental fluctuations, plants undergo several stressors during their life span, which severely impact their development and overall growth in negative aspects. Abiotic stress factors, especially moisture stress i.e shortage (drought) or excess (flooding), salinity, temperature divergence (i.e. heat and cold stress), heavy metal toxicity, etc. create osmotic and ionic imbalance inside the plant cells, which ultimately lead to devastating crop yield, sometimes crop failure. Apart from the array of abiotic stresses, various biotic stress caused by pathogens, insects, and nematodes also affect production. Therefore, to combat these major challenges in order to increase production, several novel strategies have been adapted, among which the use of nanoparticles (NPs) i.e. nanotechnology is becoming an emerging tool in various facets of the current agriculture system, nowadays. This present review will elaborately depict the deployment and mechanisms of different NPs to withstand these biotic and abiotic stresses, along with a brief overview and indication of the future research works to be oriented based on the steps provided for future research in advance NPs application through the sustainable way.

Nanobiotechnology in crop stress management: an overview of novel applications

Agricultural crops are subject to a variety of biotic and abiotic stresses that adversely affect growth and reduce the yield of crop plantss. Traditional crop stress management approaches are not capable of fulfilling the food demand of the human population which is projected to reach 10 billion by 2050. Nanobiotechnology is the application of nanotechnology in biological fields and has emerged as a sustainable approach to enhancing agricultural productivity by alleviating various plant stresses. This article reviews innovations in nanobiotechnology and its role in promoting plant growth and enhancing plant resistance/tolerance against biotic and abiotic stresses and the underlying mechanisms. Nanoparticles, synthesized through various approaches (physical, chemical and biological), induce plant resistance against these stresses by strengthening the physical barriers, improving plant photosynthesis and activating plant defense mechanisms. The nanoparticles can also upregulate the expression of stress-related genes by increasing anti-stress compounds and activating the expression of defense-related genes. The unique physico-chemical characteristics of nanoparticles enhance biochemical activity and effectiveness to cause diverse impacts on plants. Molecular mechanisms of nanobiotechnology-induced tolerance to abiotic and biotic stresses have also been highlighted. Further research is needed on efficient synthesis methods, optimization of nanoparticle dosages, application techniques and integration with other technologies, and a better understanding of their fate in agricultural systems.

Impacts of Binary Oxide Nanoparticles on the Soybean Plant and Its Rhizosphere, Associated Phytohormones, and Enzymes

The utilization of binary oxide nanoparticles is geometrically increasing due to their numerous applications. Their intentional or accidental release after usage has led to their omnipresence in the environment. The usage of sludge or fertilizer containing binary oxide nanoparticles is likely to increase the chance of the plants being exposed to these binary oxide nanoparticles. The aim of the present review is to assess the detailed positive and negative impacts of these oxide nanoparticles on the soybean plants and its rhizosphere. In this study, methods of synthesizing binary oxide nanoparticles, as well as the merits and demerits of these methods, are discussed. Furthermore, various methods of characterizing the binary oxide nanoparticles in the tissues of soybean are highlighted. These characterization techniques help to track the nanoparticles inside the soybean plant. In addition, the assessment of rhizosphere microbial communities of soybean that have been exposed to these binary oxide nanoparticles is discussed. The impacts of binary oxide nanoparticles on the leaf, stem, root, seeds, and rhizosphere of soybean plant are comprehensively discussed. The impacts of binary oxides on the bioactive compounds such as phytohormones are also highlighted. Overall, it was observed that the impacts of the oxide nanoparticles on the soybean, rhizosphere, and bioactive compounds were dose-dependent. Lastly, the way forward on research involving the interactions of binary oxide nanoparticles and soybean plants is suggested.

The Role of Nanoparticles in Response of Plants to Abiotic Stress at Physiological, Biochemical, and Molecular Levels

In recent years, the global agricultural system has been unfavorably impacted by adverse environmental changes. These changes in the climate, in turn, have altered the abiotic conditions of plants, affecting plant growth, physiology and production. Abiotic stress in plants is one of the main obstacles to global agricultural production and food security. Therefore, there is a need for the development of novel approaches to overcome these problems and achieve sustainability. Nanotechnology has emerged as one such novel approach to improve crop production, through the utilization of nanoscale products, such as nanofertilizer, nanofungicides, nanoherbicides and nanopesticides. Their ability to cross cellular barriers makes nanoparticles suitable for their application in agriculture. Since they are easily soluble, smaller, and effective for uptake by plants, nanoparticles are widely used as a modern agricultural tool. The implementation of nanoparticles has been found to be effective in improving the qualitative and quantitative aspects of crop production under various biotic and abiotic stress conditions. This review discusses various abiotic stresses to which plants are susceptible and highlights the importance of the application of nanoparticles in combating abiotic stress, in addition to the major physiological, biochemical and molecular-induced changes that can help plants tolerate stress conditions. It also addresses the potential environmental and health impacts as a result of the extensive use of nanoparticles.

Metallic and non-metallic nanoparticles from plant, animal, and fisheries wastes: potential and valorization for application in agriculture

Global agriculture is facing tremendous challenges due to climate change. The most predominant amongst these challenges are abiotic and biotic stresses caused by increased incidences of temperature extremes, drought, unseasonal flooding, and pathogens. These threats, mostly due to anthropogenic activities, resulted in severe challenges to crop and livestock production leading to substantial economic losses. It is essential to develop environmentally viable and cost-effective green processes to alleviate these stresses in the crops, livestock, and fisheries. The application of nanomaterials in farming practice to minimize nutrient losses, pest management, and enhance stress resistance capacity is of supreme importance. This paper explores innovative methods for synthesizing metallic and non-metallic nanoparticles using plants, animals, and fisheries wastes and their valorization to mitigate abiotic and biotic stresses and input use efficiency in climate-smart and stress-resilient agriculture including crop plants, livestock, and fisheries.

Fungi-derived agriculturally important nanoparticles and their application in crop stress management - Prospects and environmental risks

Nanotechnology has a wide range of agricultural applications, with emphasize on the development of novel nano-agrochemicals such as, nano-fertilizer and nano-pesticides. It has a significant impact on sustainable agriculture by increasing agricultural productivity, while reducing the use of inorganic fertilizers, pesticides, and herbicides. Nano-coating delivery methods for agrochemicals have improved agrochemical effectiveness, safety, and consistency. Biosynthesis of nanoparticles (NPs) has recently been recognized as an effective tool, contrary to chemically derived NPs, for plant abiotic and biotic stress control, and crop improvement. In this regard, fungi have tremendous scope and importance for producing biogenic NPs of various sizes, shapes, and characteristics. Fungi are potential candidates for synthesis of biogenic NPs due to their enhanced bioavailability, biological activity, and higher metal tolerance. However, their biomimetic properties and high capacity for dispersion in soil, water environments, and foods may have negative environmental consequences. Furthermore, their bioaccumulation raises significant concerns about the novel properties of nanomaterials potentially causing adverse biological effects, including toxicity. This review provides a concise outline of the growing role of fungal-mediated metal NPs synthesis, its potential applications in crop field, and associated issues of nano-pollution in soil and its future implications.

Nanofertilizer Possibilities for Healthy Soil, Water, and Food in Future: An Overview

Conventional fertilizers and pesticides are not sustainable for multiple reasons, including high delivery and usage inefficiency, considerable energy, and water inputs with adverse impact on the agroecosystem. Achieving and maintaining optimal food security is a global task that initiates agricultural approaches to be revolutionized effectively on time, as adversities in climate change, population growth, and loss of arable land may increase. Recent approaches based on nanotechnology may improve in vivo nutrient delivery to ensure the distribution of nutrients precisely, as nanoengineered particles may improve crop growth and productivity. The underlying mechanistic processes are yet to be unlayered because in coming years, the major task may be to develop novel and efficient nutrient uses in agriculture with nutrient use efficiency (NUE) to acquire optimal crop yield with ecological biodiversity, sustainable agricultural production, and agricultural socio-economy. This study highlights the potential of nanofertilizers in agricultural crops for improved plant performance productivity in case subjected to abiotic stress conditions.

Nanomaterials coupled with microRNAs for alleviating plant stress: a new opening towards sustainable agriculture

Plant growth and development is influenced by their continuous interaction with the environment. Their cellular machinery is geared to make rapid changes for adjusting the morphology and physiology to withstand the stressful changes in their surroundings. The present scenario of climate change has however intensified the occurrence and duration of stress and this is getting reflected in terms of yield loss. A number of breeding and molecular strategies are being adopted to enhance the performance of plants under abiotic stress conditions. In this context, the use of nanomaterials is gaining momentum. Nanotechnology is a versatile field and its application has been demonstrated in almost all the existing fields of science. In the agriculture sector, the use of nanoparticles is still limited, even though it has been found to increase germination and growth, enhance physiological and biochemical activities and impact gene expression. In this review, we have summarized the use and role of nanomaterial and small non-coding RNAs in crop improvement while highlighting the potential of nanomaterial assisted eco-friendly delivery of small non-coding RNAs as an innovative strategy for mitigating the effect of abiotic stress.

Cross-examination of engineered nanomaterials in crop production: Application and related implications

The review presents the current knowledge on the development and implementation of nanotechnology in crop production, giving particular attention to potential opportunities and challenges of the use of nano-sensors, nano-pesticides, and nano-fertilizers. Due to the size-dependent properties, e.g. high reactivity, targeted and controlled delivery of active ingredients, engineered nanomaterials (ENMs) are expected to be more efficient agrochemicals than conventional agents. Growing production and usage of ENMs result in the spread of ENMs in the environment. Because plants constitute an important component of the agri-ecosystem, they are subjected to the ENMs activity. A number of studies have confirmed the uptake and translocation of ENMs by plants as well as their positive/negative effects on plants. Here, these endpoints are briefly summarized to show the diversity of plant responses to ENMs. The review includes a detailed molecular analysis of ENMs-plant interactions. The transcriptomics, proteomics and metabolomics tools have been very recently employed to explore ENMs-induced effects in planta. The omics approach allows a comprehensive understanding of the specific machinery of ENMs occurring at the molecular level. The summary of data will be valuable in defining future studies on the ENMs-plant system, which is crucial for developing a suitable strategy for the ENMs usage.

Metal/Metalloid-Based Nanomaterials for Plant Abiotic Stress Tolerance: An Overview of the Mechanisms

In agriculture, abiotic stress is one of the critical issues impacting the crop productivity and yield. Such stress factors lead to the generation of reactive oxygen species, membrane damage, and other plant metabolic activities. To neutralize the harmful effects of abiotic stress, several strategies have been employed that include the utilization of nanomaterials. Nanomaterials are now gaining attention worldwide to protect plant growth against abiotic stresses such as drought, salinity, heavy metals, extreme temperatures, flooding, etc. However, their behavior is significantly impacted by the dose in which they are being used in agriculture. Furthermore, the action of nanomaterials in plants under various stresses still require understanding. Hence, with this background, the present review envisages to highlight beneficial role of nanomaterials in plants, their mode of action, and their mechanism in overcoming various abiotic stresses. It also emphasizes upon antioxidant activities of different nanomaterials and their dose-dependent variability in plants' growth under stress. Nevertheless, limitations of using nanomaterials in agriculture are also presented in this review.

The Applications of Nanotechnology in Crop Production

With the frequent occurrence of extreme climate, global agriculture is confronted with unprecedented challenges, including increased food demand and a decline in crop production. Nanotechnology is a promising way to boost crop production, enhance crop tolerance and decrease the environmental pollution. In this review, we summarize the recent findings regarding innovative nanotechnology in crop production, which could help us respond to agricultural challenges. Nanotechnology, which involves the use of nanomaterials as carriers, has a number of diverse applications in plant growth and crop production, including in nanofertilizers, nanopesticides, nanosensors and nanobiotechnology. The unique structures of nanomaterials such as high specific surface area, centralized distribution size and excellent biocompatibility facilitate the efficacy and stability of agro-chemicals. Besides, using appropriate nanomaterials in plant growth stages or stress conditions effectively promote plant growth and increase tolerance to stresses. Moreover, emerging nanotools and nanobiotechnology provide a new platform to monitor and modify crops at the molecular level.

Review: Biological functions of major latex-like proteins in plants

Major latex-like proteins (MLPs) have been identified in dicots and monocots. They are members of the birch pollen allergen Bet v 1 family as well as pathogenesis-related proteins class 10. MLPs have two main features. One is binding affinity toward various hydrophobic compounds, such as long-chain fatty acids, steroids, and systemic acquired resistance signals, via its internal hydrophobic cavity or hydrophobic residues on its surface. MLPs transport such compounds to other organs via phloem and xylem vessels and contribute to the expression of physiologically important ligands' activity in the particular organs. The second feature is responses to abiotic and biotic stresses. MLPs are involved in drought and salt tolerance through the mediation of plant hormone signaling pathways. MLPs generate resistance against pathogens by the induction of pathogenesis-related protein genes. Therefore, MLPs play crucial roles in drought and salt tolerance and resistance against pathogens. However, knowledge of MLPs is fragmented, and an overview of them is needed. Herein, we summarize the current knowledge of the biological functions of MLPs, which to our knowledge, is the first review about MLPs that has been reported.

Positive effects of metallic nanoparticles on plants: Overview of involved mechanisms

Engineered nanoparticles (NPs) are considered as potential agents for agriculture as fertilizers, growth enhancers and pesticides. Therefore, understanding the mechanisms that are responsible for their effects is important. Various studies demonstrated that the application of nontoxic concentrations can promote seed germination, enhance plant growth and increase the yield. Moreover, NPs can be used to protect plants from environmental impacts such as salt or drought stress and diminish accumulation and toxicity of heavy metals. NPs can serve as a source of micronutrients (e.g. ZnO, iron- and manganese-based NPs), thus increasing fitness and helps plants to cope with stress conditions. TiO₂ and iron-based NPs are able to delay senescence and speed-up cell division via changes in phytohormonal levels. The application of some NPs can promote the activity of enzymes such as amylase, nitrate reductase, phosphatase, phytase and carbonic anhydrases, which are involved in metabolism and nutrient acquisition. E.g. ZnO and TiO₂ NPs can stimulate chlorophyll biosynthesis and photosynthetic activity. Iron-based and CeO₂ NPs enhance stomata opening resulting in better gas exchange and CO₂ assimilation rate. NPs can also modulate oxidative stress by the stimulation of the antioxidant enzymes such peroxidases and superoxide dismutase. However, the knowledge about the fate, transformation, and accumulation of NPs in the environment and organisms is needed prior to their use in agriculture to avoid negative environmental impacts. Higher or lower toxicity of various NPs was established for microorganisms, plants or animals. In this overview, we focused on the possible mechanisms of Ag, ZnO, TiO₂, Fe-based, CeO₂, Al₂O₃, and manganese-based NPs responsible for their positive effects on plants.

Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean

Soybean, which is rich in protein and oil as well as phytochemicals, is cultivated in several climatic zones. However, its growth is markedly decreased by flooding stress, which is caused by climate change. Proteomic techniques were used for understanding the flood-response and -tolerant mechanisms in soybean. Subcellular proteomics has potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and under stress stimuli. Furthermore, post-translational modifications play important roles in stress response and tolerance to flooding stress. Although many flood-response mechanisms have been reported, flood-tolerant mechanisms have not been fully clarified for soybean because of limitations in germplasm with flooding tolerance. This review provides an update on current biochemical and molecular networks involved in soybean tolerance against flooding stress, as well as recent developments in the area of functional genomics in terms of developing flood-tolerant soybeans. This work will expedite marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.

Effects, uptake, and translocation of aluminum oxide nanoparticles in lettuce: A comparison study to phytotoxic aluminum ions

The widespread use of aluminum oxide nanoparticles (Al2O3 NPs) unavoidably causes the release of NPs into the environment, potentially having unforeseen consequences for biological processes. Due to the well-known issue of Al phytoxicity, plant interactions with Al2O3 NPs are cause for concern, but these interactions remain poorly understood. This study investigated the effects of Al2O3 NPs on lettuce (Lactuca sativa L.) to elucidate the similarities and differences in plant growth responses when compared to those of Al ions. Seed germination, root length, biomass production, and uptake of Al and nutrients were measured from hydroponically-grown lettuce with varying concentrations of Al2O3 NPs (0, 0.4, 1, and 2 mg/mL) or AlCl3 (0, 0.04, 0.4, and 1 mg/mL). The Al2O3 NPs treatments had a positive influence on root elongation, whereas AlCl3 significantly reduced emerging root lengths. While 0.4 mg/mL Al2O3 NPs promoted biomass, 1 and 2 mg/mL showed a 10.4% and 17.9% decrease in biomass, respectively, when compared to the control. Similarly, 0.4 and 1 mg/mL AlCl3 reduced biomass to 22.3% and 9.96%, respectively. Both treatments increased Al uptake by roots linearly; however, translocation of Al2O3 NPs into shoots was limited, whereas translocation of AlCl3 increased with increasing treatment concentration. Further, Al2O3 NPs adsorbed on the roots serve as adsorbents for macronutrients, promoting their absorption and uptake in plants, but not micronutrients. Calcium uptake was the most inhibited by AlCl3. A new in vivo imaging technique, with elemental analysis, confirmed that Al2O3 NPs were assimilated as particles, not ions, suggesting that the observed phytotoxicity is not due to Al ions being released from the NPs. Thus, it is concluded that Al2O3 NPs pose less phytoxicity than AlCl3, primarily due to NPs role on stimulated root growth, significant adsorption/aggregation on roots, limited lateral translocation to shoots, and increased uptake of macronutrients.

Nanoparticles: Synthesis, Morphophysiological Effects, and Proteomic Responses of Crop Plants

Plant cells are frequently challenged with a wide range of adverse environmental conditions that restrict plant growth and limit the productivity of agricultural crops. Rapid development of nanotechnology and unsystematic discharge of metal containing nanoparticles (NPs) into the environment pose a serious threat to the ecological receptors including plants. Engineered nanoparticles are synthesized by physical, chemical, biological, or hybrid methods. In addition, volcanic eruption, mechanical grinding of earthquake-generating faults in Earth's crust, ocean spray, and ultrafine cosmic dust are the natural source of NPs in the atmosphere. Untying the nature of plant interactions with NPs is fundamental for assessing their uptake and distribution, as well as evaluating phytotoxicity. Modern mass spectrometry-based proteomic techniques allow precise identification of low abundant proteins, protein-protein interactions, and in-depth analyses of cellular signaling networks. The present review highlights current understanding of plant responses to NPs exploiting high-throughput proteomics techniques. Synthesis of NPs, their morphophysiological effects on crops, and applications of proteomic techniques, are discussed in details to comprehend the underlying mechanism of NPs stress acclimation.

Recent Technological Advances in the Mass Spectrometry-based Nanomedicine Studies: An Insight from Nanoproteomics

Nanoscience becomes one of the most cutting-edge research directions in recent years since it is gradually matured from basic to applied science. Nanoparticles (NPs) and nanomaterials (NMs) play important roles in various aspects of biomedicine science, and their influences on the environment have caused a whole range of uncertainties which require extensive attention. Due to the quantitative and dynamic information provided for human proteome, mass spectrometry (MS)-based quantitative proteomic technique has been a powerful tool for nanomedicine study. In this article, recent trends of progress and development in the nanomedicine of proteomics were discussed from quantification techniques and publicly available resources or tools. First, a variety of popular protein quantification techniques including labeling and label-free strategies applied to nanomedicine studies are overviewed and systematically discussed. Then, numerous protein profiling tools for data processing and postbiological statistical analysis and publicly available data repositories for providing enrichment MS raw data information sources are also discussed.

Quantitative proteomic analysis of HeLa cells in response to biocompatible Fe2C@C nanoparticles: 16O/18O-labelling & HPLC-ESI-orbit-trap profiling approach

The effective detection of molecular biomarkers, such as proteins, lipids, carbohydrates, and pathogens, in a living body is a huge challenge in the field of nanomedicine. Here, we have investigated the comparative quantitative proteomics analysis of the molecular response of HeLa cells to biocompatible Fe2C@C nanoparticles (NPs) using 16O/18O isotopic labelling of the cell culture. The relative binding efficiency of proteins to Fe2C@C NPs was calculated. HPLC-ESI-orbit-trap analysis found 51 differentially expressed proteins, out of which 23 were over-expressed and 28 down-regulated. This study showed that Fe2C@C NPs alter the expression of the proteins involved in endocytosis, cell-cycle regulation, and cell membrane protrusion. Further, the quantification and validation of the mass spectrometry (MS) results was successfully confirmed by western blot analysis of cytochrome C. The change in the expression of proteins can be useful for early stage disease diagnoses and the development of tailored therapeutic strategies. This study is the first large-scale characterization of low abundance proteins on Fe2C@C NPs, providing the biochemical basis for the assessment of the suitability of magnetic NPs as biomedical markers and emerging functional probes.

Proteomic Analysis of Calcium Effects on Soybean Root Tip under Flooding and Drought Stresses

Flooding and drought are disadvantageous environmental conditions that induce cytosolic calcium in soybean. To explore the effects of flooding- and drought-induced increases in calcium, a gel-free/label-free proteomic analysis was performed. Cytosolic calcium was decreased by blocking calcium channels in the endoplasmic reticulum (ER) and plasma membrane under both stresses. Calnexin, protein disulfide isomerase, heat shock proteins and thioredoxin were predominantly affected as the ER proteins in response to calcium, and ER-associated degradation-related proteins of HCP-like superfamily protein were up-regulated under stress exposure and then down-regulated. Glycolysis, fermentation, the tricarboxylic acid cycle and amino acid metabolism were mainly induced as the types of cellular metabolism in response to calcium under both stresses. Pyruvate decarboxylase was increased and decreased under flooding and drought, respectively, and was further decreased by the reduction of cytosolic calcium; however, it was recovered by exogenous calcium under both stresses. Furthermore, pyruvate decarboxylase activity was increased under flooding, but decreased under drought. These results suggest that calcium is involved in protein folding in the ER, and ER-associated degradation might alleviate ER stress during the early stage of both stresses. Furthermore, calcium appears to modify energy metabolism, and pyruvate decarboxylase may be a key enzyme in this process under flooding and drought.

Improvement of Soybean Products Through the Response Mechanism Analysis Using Proteomic Technique

Soybean is rich in protein/vegetable oil and contains several phytochemicals such as isoflavones and phenolic compounds. Because of the predominated nutritional values, soybean is considered as traditional health benefit food. Soybean is a widely cultivated crop; however, its growth and yield are markedly affected by adverse environmental conditions. Proteomic techniques make it feasible to map protein profiles both during soybean growth and under unfavorable conditions. The stress-responsive mechanisms during soybean growth have been uncovered with the help of proteomic studies. In this review, the history of soybean as food and the morphology/physiology of soybean are described. The utilization of proteomics during soybean germination and development is summarized. In addition, the stress-responsive mechanisms explored using proteomic techniques are reviewed in soybean.

Insights into the Response of Soybean Mitochondrial Proteins to Various Sizes of Aluminum Oxide Nanoparticles under Flooding Stress

Rapid developments in nanotechnology have led to the increasing use of nanoparticles (NPs) in the agricultural sector. For possible interactions between NPs and crops under flooding stress to be investigated, the molecular mechanisms in soybeans affected by exposure to various sizes of Al2O3 NPs were analyzed using a proteomic technique. In plants exposed to 30-60 nm Al2O3 NPs, the length of the root including hypocotyl was increased, and proteins related to glycolysis were suppressed. Exposure to 30-60 nm Al2O3 NPs mediated the scavenging activity of cells by regulating the ascorbate/glutathione pathway. Hierarchical clustering analysis indicated that ribosomal proteins were also increased upon exposure to flooding-stressed plants with 30-60 nm Al2O3 NPs. Mitochondrion was the target organelle of Al2O3 NPs under flooding-stress conditions. Mitochondrial proteomic analysis revealed that the abundance of voltage-dependent anion channel protein was increased upon exposure to flooding-stressed soybeans with 135 nm Al2O3 NPs, indicating the permeability of the mitochondrial membrane was increased. Furthermore, isocitrate dehydrogenase was increased upon exposure of plants to 5 nm Al2O3 NPs under flooding conditions. These results suggest that Al2O3 NPs of various sizes affect mitochondrial proteins under flooding stress by regulating membrane permeability and tricarboxylic acid cycle activity.

Proteomic analysis of soybean root exposed to varying sizes of silver nanoparticles under flooding stress

Silver nanoparticles (Ag-NPs) are excessively used as antibacterial agents; however, environmental interaction specifically with the plants remain uncertain. To study the size-dependent effects of Ag-NPs on soybean under flooding, a proteomic technique was used. Morphological analysis revealed that treatment with Ag-NPs of 15nm promoted soybean growth under flooding compared to 2 and 50-80nm. A total of 228 common proteins that significantly changed in abundance under flooding without and with Ag-NPs of 2, 15, and 50-80nm. Under varying sizes of Ag-NPs, number of protein synthesis related proteins decreased compared to flooding while number of amino acid synthesis related proteins were increased under Ag-NPs of 15nm. Hierarchical clustering identified the ribosomal proteins that increased under Ag-NPs of 15nm while decreased under other sizes. In silico protein-protein interaction indicated the beta ketoacyl reducatse 1 as the most interacted protein under Ag-NPs of 15nm while least interacted under other sizes. The beta ketoacyl reductase 1 was up-regulated under Ag-NPs of 15nm while its enzyme activity was decreased. These results suggest that the different sizes of Ag-NPs might affect the soybean growth under flooding by regulating the proteins related to amino acid synthesis and wax formation.

BIOLOGICAL SIGNIFICANCE

This study highlighted the response of soybean proteins towards varying sizes of Ag NPs under flooding stress using gel-free proteomic technique. The Ag NPs of 15nm improved the length of root including hypocotyl of soybean. The proteins related to protein metabolism, cell division/organization, and amino acid metabolism were differentially changed under the varying sizes of Ag NPs. The protein synthesis-related proteins were decreased while amino acid metabolism-related proteins were increased under varying sizes of Ag NPs. The ribosomal proteins were increased under Ag NPs of 15nm. The beta ketoacyl reductase 1 was identified as the most interacted protein under varying sizes of Ag NPs. The mRNA expression level of beta ketoacyl reductase was up-regulated under Ag NPs of 15nm while its activity was decreased. These results suggest that the Ag NPs of 15nm improved the soybean growth under flooding stress by increasing the proteins related to amino acid synthesis and waxes formation.

Gel-free/label-free proteomic analysis of wheat shoot in stress tolerant varieties under iron nanoparticles exposure

Iron nanoparticles (Fe NPs) have stimulatory effects on the germination ratio and plant growth of wheat. To elucidate the effects of Fe NPs on shoot of drought tolerant Pakistan-13 and salt tolerant NARC-11, a gel-free/label-free proteomic technique was used. The weights/lengths of seedling, shoot, and root of wheat varieties were increased on 5ppm Fe NPs exposure. The number of proteins related to photosynthesis and protein metabolism was decreased and increased in drought tolerant variety and salt tolerant variety, respectively, treated with Fe NPs compared to untreated plants. Differentially changed proteins in drought tolerant variety and salt tolerant variety were mainly related to photosynthesis. Out of photosynthesis related proteins, light reaction was enhanced in salt tolerant variety compared to drought tolerant variety on Fe NPs exposure. The abundance of ribulose bisphosphate carboxylase/oxygenase small chain in drought tolerant variety was higher than that in salt tolerant variety; however, in salt tolerant variety, it was increased 3 fold by Fe NPs exposure compared to untreated plant. These results suggest that Fe NPs improve the growth of wheat seedling, which might be associated with the increase of protein abundance in photosynthesis in salt tolerant variety.

Quantitative proteomic analysis of post-flooding recovery in soybean root exposed to aluminum oxide nanoparticles

Aluminum oxide nanoparticles (Al2O3 NPs) are used in various commercial and agricultural products. Soybean exhibits severe reduction in growth under flooding condition. To examine the effects of Al2O3 NPs on the recovery of soybean from flooding, proteomic analysis was performed. Survival percentage and weight/length of root including hypocotyl were improved after 2 and 4days of flooding with 50ppm Al2O3 NPs leading to recovery as compared to flooding. A total of 211 common proteins were changed in abundance during the recovery period after treatment without or with Al2O3 NPs. These proteins were related to protein synthesis, stress, cell wall, and signaling. Among the identified stress-related proteins, S-adenosyl-l-methionine dependent methyltransferases were recovered from flooding with Al2O3 NPs. Hierarchical clustering divided the identified proteins into three clusters. Cluster II exhibited the greatest change in proteins related to protein synthesis, transport, and development during the recovery from flooding with Al2O3 NPs. However, activity of enolase remained unchanged during flooding leading to subsequent recovery with Al2O3 NPs. These results suggest that S-adenosyl-l-methionine dependent methyltransferases and enolase might be involved in mediating recovery responses by Al2O3 NPs.

BIOLOGICAL SIGNIFICANCE

This study highlighted the role of Al2O3 NPs in recovery of soybean seedlings from flooding stress using gel-free proteomic technique. The key findings of this study are as follows: (i) survival percentage was enhanced at 50ppm Al2O3 NPs during the recovery stage; (ii) seedling weight and weight/length of root including hypocotyl improved at 50ppm Al2O3 NPs during the period of recovery; (iii) protein synthesis and stress related proteins were increased on recovery after flooding without or with Al2O3 NPs; (iv) the abundance of S-adenosyl-l-methionine dependent methyltransferases recovered from flooding with Al2O3 NPs; (v) glycolysis related proteins amplified under flooding with Al2O3 NPs; (vi) enolase enzyme remained unchanged during flooding leading to subsequent recovery from flooding with Al2O3 NPs. Collectively, these results suggest that S-adenosyl-l-methionine dependent methyltransferases and enolase are involved in response to flooding with Al2O3 NPs and might be helpful in recovery from flooding stress.

Toxicity of heavy metals and metal-containing nanoparticles on plants

Plants are under the continual threat of changing climatic conditions that are associated with various types of abiotic stresses. In particular, heavy metal contamination is a major environmental concern that restricts plant growth. Plants absorb heavy metals along with essential elements from the soil and have evolved different strategies to cope with the accumulation of heavy metals. The use of proteomic techniques is an effective approach to investigate and identify the biological mechanisms and pathways affected by heavy metals and metal-containing nanoparticles. The present review focuses on recent advances and summarizes the results from proteomic studies aimed at understanding the response mechanisms of plants under heavy metal and metal-containing nanoparticle stress. Transport of heavy metal ions is regulated through the cell wall and plasma membrane and then sequestered in the vacuole. In addition, the role of different metal chelators involved in the detoxification and sequestration of heavy metals is critically reviewed, and changes in protein profiles of plants exposed to metal-containing nanoparticles are discussed in detail. Finally, strategies for gaining new insights into plant tolerance mechanisms to heavy metal and metal-containing nanoparticle stress are presented. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Plant Responses to Nanoparticle Stress

With the rapid advancement in nanotechnology, release of nanoscale materials into the environment is inevitable. Such contamination may negatively influence the functioning of the ecosystems. Many manufactured nanoparticles (NPs) contain heavy metals, which can cause soil and water contamination. Proteomic techniques have contributed substantially in understanding the molecular mechanisms of plant responses against various stresses by providing a link between gene expression and cell metabolism. As the coding regions of genome are responsible for plant adaptation to adverse conditions, protein signatures provide insights into the phytotoxicity of NPs at proteome level. This review summarizes the recent contributions of plant proteomic research to elaborate the complex molecular pathways of plant response to NPs stress.