Proteomic Analysis of Irradiation with Millimeter Waves on Soybean Growth under Flooding Conditions

Protein-Based Mechanism of Wheat Growth Under Salt Stress in Seeds Irradiated with Millimeter Waves

Wheat is one of the most extensively grown crops in the world; however, its productivity is reduced due to salinity. This study focused on millimeter wave (MMW) irradiation to clarify the salt-stress tolerance mechanism in wheat. In the present study, wheat-root growth, which was suppressed to 77.6% of the control level under salt stress, was recovered to the control level by MMW irradiation. To reveal the salt-stress tolerance mechanism of MMW irradiation on wheat, a proteomic analysis was conducted. Proteins related to cell cycle, proliferation, and transport in biological processes, as well as proteins related to the nucleus, cytoskeleton, and cytoplasm within cellular components, were inversely correlated with the number of proteins. The results of the proteomic analysis were verified by immunoblot and other analyses. Among the proteins related to the scavenging reactive-oxygen species, superoxide dismutase and glutathione reductase accumulated under salt stress and further increased in the MMW-irradiated wheat. Among pathogen-related proteins, pathogenesis-related protein 1 and the Bowman-Birk proteinase inhibitor decreased under salt stress and recovered to the control level in the MMW-irradiated wheat. The present results indicate that MMW irradiation of wheat seeds improves plant-growth recovery from salt stress through regulating the reactive oxygen species-scavenging system and the pathogen-related proteins. These genes may contribute to the development of salt-stress-tolerant wheat through marker-assisted breeding and genome editing.

Application of multiomics analysis to plant flooding response

Flooding, as a natural disaster, plays a pivotal role in constraining the growth and development of plants. Flooding stress, including submergence and waterlogging, not only induces oxygen, light, and nutrient deprivation, but also alters soil properties through prolonged inundation, further impeding plant growth and development. However, hypoxia (or anoxia) is the most serious and direct damage to plants caused by flooding. Moreover, flooding disrupts the structural integrity of plant cell walls and compromises endoplasmic reticulum functionality, while hindering nutrient absorption and shifting metabolic processes from normal aerobic respiration to anaerobic respiration. It can be asserted that flooding exerts comprehensive effects on plants encompassing phenotypic changes, transcriptional alterations, protein dynamics, and metabolic shifts. To adapt to flooding environments, plants employ corresponding adaptive mechanisms at the phenotypic level while modulating transcriptomic profiles, proteomic characteristics, and metabolite levels. Hence, this study provides a comprehensive analysis of transcriptomic, proteomic, and metabolomics investigations conducted on flooding stress on model plants and major crops, elucidating their response mechanisms from diverse omics perspectives.

Millmeter-wave irradiation regulates mRNA-expression and the ubiquitin-proteasome system in wheat exposed to flooding stress

The irradiation with millimeter-wave (MMW) of wheat seeds promotes root growth under flooding stress; however, its role is not completely clarified. Nuclear proteomics was performed, to reveal the role of MMW irradiation in enhancing flooding tolerance. The purity of nuclear fractions purified from roots was verified. Histone, which is a protein marker for nuclear-purification efficiency, was enriched; and cytosolic ascorbate peroxidase was reduced in the nuclear fraction. The principal-component analysis of proteome displayed that the irradiation of seeds affected nuclear proteins in roots grown under flooding stress. Proteins detected using proteomic analysis were verified using immunoblot analysis. Histone H3 accumulated under flooding stress; however, it decreased to the control level by irradiation. Whereas the ubiquitin accumulated in roots grown under stress when seeds were irradiated. These results suggest that MMW irradiation improves wheat-root growth under flooding stress through the regulation of mRNA-expression level and the ubiquitin-proteasome system. SIGNIFICANCE: To reveal the role of millimeter-wave irradiation in enhancing flooding tolerance in wheat, nuclear proteomics was performed. The principal-component analysis of proteome displayed that irradiation of seeds affected nuclear proteins in roots grown under flooding stress. Proteins detected using proteomic analysis were verified using immunoblot analysis. Histone H3 accumulated under flooding stress; however, it decreased to the control level with irradiation. Whereas the ubiquitin accumulated in roots grown under stress when seeds were irradiated. These results suggest that millimeter-wave irradiation improves wheat-root growth under flooding stress through the regulation of mRNA-expression level and the ubiquitin-proteasome system.

Membrane Proteomics to Understand Enhancement Effects of Millimeter-Wave Irradiation on Wheat Root under Flooding Stress

Millimeter-wave irradiation of wheat seeds enhances the growth of roots under flooding stress, but its mechanism is not clearly understood. To understand the role of millimeter-wave irradiation on root-growth enhancement, membrane proteomics was performed. Membrane fractions purified from wheat roots were evaluated for purity. H⁺-ATPase and calnexin, which are protein markers for membrane-purification efficiency, were enriched in a membrane fraction. A principal-component analysis of the proteomic results indicated that the millimeter-wave irradiation of seeds affects membrane proteins in grown roots. Proteins identified using proteomic analysis were confirmed using immunoblot or polymerase chain reaction analyses. The abundance of cellulose synthetase, which is a plasma-membrane protein, decreased under flooding stress; however, it increased with millimeter-wave irradiation. On the other hand, the abundance of calnexin and V-ATPase, which are proteins in the endoplasmic reticulum and vacuolar, increased under flooding stress; however, it decreased with millimeter-wave irradiation. Furthermore, NADH dehydrogenase, which is found in mitochondria membranes, was upregulated due to flooding stress but downregulated following millimeter-wave irradiation even under flooding stress. The ATP content showed a similar trend toward change in NADH dehydrogenase expression. These results suggest that millimeter-wave irradiation improves the root growth of wheat via the transitions of proteins in the plasma membrane, endoplasmic reticulum, vacuolar, and mitochondria.

The intervention of classical and molecular breeding approaches to enhance flooding stress tolerance in soybean - An review

Abiotic stresses and climate changes cause severe loss of yield and quality of crops and reduce the production area worldwide. Flooding stress curtails soybean growth, yield, and quality and ultimately threatens the global food supply chain. Flooding tolerance is a multigenic trait. Tremendous research in molecular breeding explored the potential genomic regions governing flood tolerance in soybean. The most robust way to develop flooding tolerance in soybean is by using molecular methods, including quantitative trait loci (QTL) mapping, identification of transcriptomes, transcription factor analysis, CRISPR/Cas9, and to some extent, genome-wide association studies (GWAS), and multi-omics techniques. These powerful molecular tools have deepened our knowledge about the molecular mechanism of flooding stress tolerance. Besides all this, using conventional breeding methods (hybridization, introduction, and backcrossing) and other agronomic practices is also helpful in combating the rising flooding threats to the soybean crop. The current review aims to summarize recent advancements in breeding flood-tolerant soybean, mainly by using molecular and conventional tools and their prospects. This updated picture will be a treasure trove for future researchers to comprehend the foundation of flooding tolerance in soybean and cover the given research gaps to develop tolerant soybean cultivars able to sustain growth under extreme climatic changes.

Crop Proteomics under Abiotic Stress: From Data to Insights

Food security is a major challenge in the present world due to erratic weather and climatic changes. Environmental stress negatively affects plant growth and development which leads to reduced crop yields. Technological advancements have caused remarkable improvements in crop-breeding programs. Proteins have an indispensable role in developing stress resilience and tolerance in crops. Genomic and biotechnological advancements have made the process of crop improvement more accurate and targeted. Proteomic studies provide the information required for such targeted approaches. The crosstalk among cellular components is being analyzed by subcellular proteomics. Additionally, the functional diversity of proteins is being unraveled by post-translational modifications during abiotic stress. The exploration of precise cellular responses and the networking among different cellular organelles help in the prediction of signaling pathways and protein-protein interactions. High-throughput mass-spectrometry-based protein studies are now possible due to incremental advancements in mass-spectrometry techniques, sample protocols, and bioinformatic tools as well as the increasing availability of plant genome sequence information for multiple species. In this review, the key role of proteomic analysis in identifying the abiotic-stress-responsive mechanisms in various crops was summarized. The development and availability of advanced computational tools were discussed in detail. The highly variable protein responses among different crops have provided a wide avenue for molecular-marker-assisted genetic buildup studies to develop smart, high-yielding, and stress-tolerant varieties to cope with food-security challenges.

Proteomic and Biochemical Approaches Elucidate the Role of Millimeter-Wave Irradiation in Wheat Growth under Flooding Stress

Flooding impairs wheat growth and considerably affects yield productivity worldwide. On the other hand, irradiation with millimeter waves enhanced the growth of chickpea and soybean under flooding stress. In the current work, millimeter-wave irradiation notably enhanced wheat growth, even under flooding stress. To explore the protective mechanisms of millimeter-wave irradiation on wheat under flooding, quantitative proteomics was performed. According to functional categorization, proteins whose abundances were changed significantly with and without irradiation under flooding stress were correlated to glycolysis, reactive-oxygen species scavenging, cell organization, and hormonal metabolism. Immunoblot analysis confirmed that fructose-bisphosphate aldolase and β tubulin accumulated in root and leaf under flooding; however, even in such condition, their accumulations were recovered to the control level in irradiated wheat. The abundance of ascorbate peroxidase increased in leaf under flooding and recovered to the control level in irradiated wheat. Because the abundance of auxin-related proteins changed with millimeter-wave irradiation, auxin was applied to wheat under flooding, resulting in the application of auxin improving its growth, even in such condition. These results suggest that millimeter-wave irradiation on wheat seeds improves the recovery of plant growth from flooding via the regulation of glycolysis, reactive-oxygen species scavenging, and cell organization. Additionally, millimeter-wave irradiation could promote tolerance against flooding through the regulation of auxin contents in wheat.

Morphological, Biochemical, and Proteomic Analyses to Understand the Promotive Effects of Plant-Derived Smoke Solution on Wheat Growth under Flooding Stress

Wheat is an important staple food crop for one-third of the global population; however, its growth is reduced by flooding. On the other hand, a plant-derived smoke solution enhances plant growth; however, its mechanism is not fully understood. To reveal the effects of the plant-derived smoke solution on wheat under flooding, morphological, biochemical, and proteomic analyses were conducted. The plant-derived smoke solution improved wheat-leaf growth, even under flooding. According to the functional categorization of proteomic results, oppositely changed proteins were correlated with photosynthesis, glycolysis, biotic stress, and amino-acid metabolism with or without the plant-derived smoke solution under flooding. Immunoblot analysis confirmed that RuBisCO activase and RuBisCO large/small subunits, which decreased under flooding, were recovered by the application of the plant-derived smoke solution. Furthermore, the contents of chlorophylls a and b significantly decreased by flooding stress; however, they were recovered by the application of the plant-derived smoke solution. In glycolysis, fructose-bisphosphate aldolase and glyceraldehyde-3-phosphate dehydrogenase decreased with the application of the plant-derived smoke solution under flooding as compared with flooding alone. Additionally, glutamine, glutamic acid, aspartic acid, and serine decreased under flooding; however, they were recovered by the plant-derived smoke solution. These results suggest that the application of the plant-derived smoke solution improves the recovery of wheat growth through the regulation of photosynthesis and glycolysis even under flooding conditions. Furthermore, the plant-derived smoke solution might promote wheat tolerance against flooding stress through the regulation of amino-acid metabolism.

Glyphosate-induced GhAG2 is involved in resistance to salt stress in cotton

KEY MESSAGE

The transcription of GhAG2 was strongly enhanced by glyphosate treatment. Overexpression of GhAG2 could improve plant tolerance to salt and salicylic acid stress. Although glyphosate has been widely used as an herbicide over the past decade owing to its high efficacy on weed controls and worldwide commercialization of glyphosate-resistant crops, little is known about the glyphosate-induced responses and transcriptional changes in cotton plants. Here, we report the identification of 26 differentially expressed genes after glyphosate treatment, among which, six highly up-regulated sequences share homology to cotton expressed sequence tags (ESTs) responsive to abiotic stresses. In addition, we cloned GhAG2, a gene whose transcription was strongly enhanced by glyphosate treatment and other abiotic stresses. Transgenic GhAG2 plants showed improved tolerance to salt, and salicylic acid (SA) stress. The results could open the door to exploring the function of the GhAG2 proteins, the glyphosate-induced transcriptional profiles, and the physiological biochemical responses in cotton and other crops. GhAG2 could also be used to improve salt stress tolerance through breeding and biotechnology in crops. Furthermore, these results could provide guidelines to develop a glyphosate-inducible system for controlled expression of targeted genes in plants.

Morphophysiological and Proteomic Responses on Plants of Irradiation with Electromagnetic Waves

Electromagnetic energy is the backbone of wireless communication systems, and its progressive use has resulted in impacts on a wide range of biological systems. The consequences of electromagnetic energy absorption on plants are insufficiently addressed. In the agricultural area, electromagnetic-wave irradiation has been used to develop crop varieties, manage insect pests, monitor fertilizer efficiency, and preserve agricultural produce. According to different frequencies and wavelengths, electromagnetic waves are typically divided into eight spectral bands, including audio waves, radio waves, microwaves, infrared, visible light, ultraviolet, X-rays, and gamma rays. In this review, among these electromagnetic waves, effects of millimeter waves, ultraviolet, and gamma rays on plants are outlined, and their response mechanisms in plants through proteomic approaches are summarized. Furthermore, remarkable advancements of irradiating plants with electromagnetic waves, especially ultraviolet, are addressed, which shed light on future research in the electromagnetic field.

Proteomic and Biological Analyses Reveal the Effect on Growth under Flooding Stress of Chickpea Irradiated with Millimeter Waves

Chickpea cultivated on marginal lands in arid and semiarid tropics is one of the food legumes, and its growth is reduced by flooding stress. Millimeter-wave irradiation has influences on organisms, and it improves the growth of plants such as soybean. To reveal the dynamic effects of millimeter-wave irradiation on chickpea under flooding, gel- and label-free proteomic analysis was conducted. Millimeter-wave irradiation improved chickpea growth and its tolerance to flooding stress. According to functional categorization, oppositely changed proteins were correlated with photosynthesis, fermentation, and protein degradation. Immunoblot analysis confirmed that RuBisCO activase and large subunits decreased in leaves under flooding; however, they are recovered in irradiated chickpea even if it was in this condition. The activity and accumulation of alcohol dehydrogenase increased in roots under flooding; however, this followed the same pattern. Cell death was significantly increased and decreased by flooding on unirradiated and irradiated chickpeas, respectively. These findings suggest that irradiation with millimeter waves on chickpea seeds improves the recovery of plant growth through regulation of photosynthesis in leaves and fermentation in roots. Furthermore, millimeter-wave irradiation might promote chickpea tolerance under flooding via the regulation of cell death.

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.

A comparative proteomic analysis of engineered and bio synthesized silver nanoparticles on soybean seedlings

Nanoparticles (NPs) are synthesized by different methods and response mechanism of plants varied towards NPs based on their origin. To study the effects of bio synthesized (BS) and chemically synthesized (CS) silver NPs on soybean, a gel-free/ label-free proteomic technique was used. Length of root and hypocotyl was enhanced by BS compared to CS silver NPs. 10 ppm BS silver NPs enhanced the length of root and hypocotyl compared to 1 and 50 ppm. A total of 190 and 173 differentially changed proteins were identified in BS and CS silver NPs treated soybean, respectively. Twenty proteins commonly changed between BS and CS silver NPs treated soybean. Differentially-changed proteins were associated with protein-degradation and stress according to functional categorization. From proteomics, abundances of peroxidases were increased under CS silver NPs. Immunoblot analysis depicted that accumulation of ascorbate peroxidase, glutathione reductase, and peroxiredoxin remained unchanged under both BS and CS silver NPs. ATP content decreased under CS silver NPs compared to BS silver NPs. ADH activity increased in CS silver NPs treated soybean. These results suggest that BS silver NPs enhanced the growth of soybean by regulating proteins related to protein-degradation and ATP contents, which are negatively affected by CS silver NPs. BIOLOGICAL SIGNIFICANCE: This study highlighted the response mechanism of soybean towards bio synthesized (BS) and chemically synthesized (CS) silver nanoparticles (NPs) using a gel-free/ label-free proteomics technique. Length of root and hypocotyl was enhanced by BS silver NPs compared to CS silver NPs. 10 ppm BS silver NPs enhanced the length of root and hypocotyl compared to other concentrations. Differentially changed proteins were associated with protein degradation and stress. From the proteomics, the abundances of peroxidases were increased under CS silver NPs. Immunoblot analysis depicted that accumulation of ascorbate peroxidase, glutathione reductase, and peroxiredoxin remained unchanged under both BS and CS silver NPs. ATP content decreased under CS silver NPs compared to BS silver NPs. ADH activity increased in CS silver NPs compared to BS silver NPs treated soybean. These results suggest that the BS silver NPs enhanced the growth of soybean by regulating the proteins related to protein degradation and ATP contents, which are negatively affected by the CS silver NPs.

Plant-derived smoke enhances plant growth through ornithine-synthesis pathway and ubiquitin-proteasome pathway in soybean

To investigate the mechanism of promotive effect of plant-derived smoke on the soybean growth, a gel-free/label-free proteomics was performed. Smoke solutions were irrigated on soybean or supplied simultaneously with flooding stress. Morphological and physiological analyses were performed for the confirmation of proteomic result. Metabolomic change was investigated to correlate proteomic change with metabolism regulation. Under normal condition, the length of root including hypocotyl increased in soybean treated with 2000 ppm plant-derived smoke within 4 days, as well as nitric oxide content. Proteins related to protein synthesis especially arginine metabolism were altered; metabolites related to amino acid, carboxylic acids, and sugars were mostly altered. Integrated analysis of omics data indicated that plant-derived smoke regulated nitrogen‑carbon transformation through ornithine synthesis pathway and promoted soybean normal growth. Under flooding, the number of lateral roots increased with root tip degradation in soybean treated with smoke solutions. Proteins related to ubiquitin-proteasome pathway were altered and led to sacrifice-for-survival-mechanism-driven degradation of root tip in soybean, which enabled accumulation of metabolites and guaranteed lateral root development during soybean recovery after flooding. These findings suggest that plant-derived smoke improves early stage of growth in soybean with regulation of ornithine-synthesis pathway and ubiquitin-proteasome pathway. BIOLOGICAL SIGNIFICANCE: Plant-derived smoke plays a key role in crop growth, however, the understanding of soybean in response to smoke treatment remains premature. Therefore, gel-free/label-free proteomic analysis was used for comprehensive study on the dual effect of smoke to soybean under normal and flooding conditions. Under normal condition, plant-derived smoke regulated nitrogen‑carbon transformation through ornithine synthesis pathway and resulted in the increase of the length of root including hypocotyl in soybean within 4 days. Under flooding condition, plant-derived smoke induced inhibition of ubiquitin-proteasome pathway and led to sacrifice-for-survival-mechanism-driven degradation of root tip in soybean, which enabled accumulation of metabolites and promoted lateral root development during soybean recovery after flooding.