iTRAQ protein profile analysis of sugar beet under salt stress: different coping mechanisms in leaves and roots

Application of proteomics in investigating the responses of plant to abiotic stresses

MAIN CONCLUSION

This review summarizes the application of proteomic techniques in investigating the responses of plant to abiotic stresses. In the natural environment, the plants are exposed to a diverse range of adverse abiotic factors that significantly impact their growth and development. The plants have evolved intricate stress response mechanisms at the genetic, protein, metabolic, and phenotypic levels to mitigate damage caused by unfavorable conditions. Proteomics serves as an effective tool for studying protein changes in plants and provides valuable insights into the physiological mechanisms underlying plant stress resistance. Several proteins involved in abiotic stress responses have been identified in plants, including transcription factors, protein kinases, ATP synthases, heat shock proteins, redox proteins, and enzymes in secondary metabolite pathways. Medicinal plants are a unique category of crops capable of synthesizing secondary metabolites, which play a crucial role in resisting abiotic stress and exhibit changes in content under stress conditions. In this review, we present an overview of proteomic tools employed for investigating the responses of plants to abiotic stresses and summarize alterations observed at the protein level under various abiotic stresses such as signal transduction, oxidative damage, carbohydrate and energy metabolism, protein and amino acid metabolism, cellular homeostasis, and enzyme involvement in secondary metabolism. This work aims to facilitate the application of proteomics techniques in plants research while enhancing our understanding of the response mechanisms exhibited by these plants towards abiotic stresses.

Effect of the Aqueous Quercetin Solution on the Physiological Properties of Virginia Mallow (Ripariosida hermaphrodita) Grown Under Salt Stress Conditions

The current increase in energy demand, along with the deepening climate crisis, has led to the need for alternative energy sources. One of these is the cultivation of energy crops. In turn, issues related to the deepening problem of soil salinization are an important aspect of environmental protection on a global scale. New species and innovative solutions are sought to support the effective cultivation of energy crops, including in saline areas. The purpose of the study was to evaluate the effect of the foliar application of an aqueous quercetin solution applied in different doses (1%, 3% and 5%) on the physiological properties of Virginia Mallow plants subjected to salt stress conditions. The experiment was carried out as a pot experiment. The results obtained were related to two types of plants treated as a control sample. In one case, they were grown with the addition of quercetin alone, without salt stress. The other group was grown without quercetin and without salt. Quercetin is a phenolic compound that plays an important physiological and biochemical role in plants. Salinity caused a significant decrease in physiological indices in Virginia Mallow leaves. Foliar application of an aqueous quercetin solution mitigated the negative impact of salt on plants, the most stimulating effect being demonstrated at a dose of 5.0%.

Based proteomics analyses reveal response mechanisms of Apis mellifera (Hymenoptera: Apidae) against the heat stress

Heat stress can significantly affect the survival, metabolism, and reproduction of honeybees. It is important to understand the proteomic changes of honeybees under heat stress to understand the molecular mechanism behind heat resistance. However, the proteomic changes of honeybees under heat stress are poorly understood. We analyzed the proteomic changes of Apis mellifera Ligustica (Hymenoptera: Apidae) under heat stress using mass spectrometry-based proteomics with TMT (Tandem mass tags) stable isotope labeling. A total of 3,799 proteins were identified, 85 of which differentially abundance between experimental groups. The most significant categories affected by heat stress were associated with transcription and translation processes, metabolism, and stress-resistant pathways. We found that heat stress altered the protein profiles in A. mellifera, with momentous resist proteins being upregulated in heat groups. These results show a proof of molecular details that A. mellifera can respond to heat stress by increasing resist proteins. Our findings add research basis for studying the molecular mechanisms of honeybees' resistance to heat stress. The differentially expressed proteins identified in this study can be used as biomarkers of heat stress in bees, and provide a foundation for future research on honeybees under heat stress. Our in-depth proteomic analysis provides new insights into how bees cope with heat stress.

Salt Tolerance in Sugar Beet: From Impact Analysis to Adaptive Mechanisms and Future Research

The continuous global escalation of soil salinization areas presents severe challenges to the stability and growth of agricultural development across the world. In-depth research on sugar beet (Beta vulgaris L.), an important economic and sugar crop with salt tolerance characteristics, is crucial for to determine its salt-tolerance mechanisms, which has important practical implications for production. This review summarizes the multifaceted effects of salt stress on sugar beet, ranging from individual plant responses to cellular and molecular adaptations. Sugar beet exhibits robust salt-tolerance mechanisms, including osmotic regulation, ion balance management, and the compartmentalization of toxic ions. Omics technologies, including genomics, transcriptomics, proteomics, post-translational modification omics and metabolomics, have played crucial roles in elucidating these mechanisms. Key genes and pathways involved in salt tolerance in sugar beet have been identified, paving the way for targeted breeding strategies and biotechnological advancements. Understanding these mechanisms not only enhances our knowledge of sugar beet's adaptation strategies but also provides insights for improving salt tolerance in other crops. Future studies should focus on analyzing gene expression changes in sugar beet under salt stress to gain insight into the molecular aspects of its salt-tolerance mechanisms. Meanwhile, the effects of different environmental conditions on sugar beet adaptation strategies should also be investigated to improve their growth potential in salinized soils.

Tandem mass tag (TMT)-based quantitative proteomics analysis reveals the different responses of contrasting alfalfa varieties to drought stress

BACKGROUND

Drought stress restricts the growth, distribution and productivity of alfalfa (Medicago sativa L.). In order to study the response differences of alfalfa cultivars to drought stress, we previously carried out physiological and molecular comparative analysis on two alfalfa varieties with contrasting drought resistance (relatively drought-tolerant Longdong and drought-sensitive Algonquin). However, the differences in proteomic factors of the two varieties in response to drought stress still need to be further studied. Therefore, TMT-based quantitative proteomic analysis was performed using leaf tissues of the two alfalfa cultivars to identify and uncover differentially abundant proteins (DAPs).

RESULTS

In total, 677 DAPs were identified in Algonquin and 277 in Longdong under drought stress. Subsequently, we conducted various bioinformatics analysis on these DAPs, including subcellular location, functional classification and biological pathway enrichment. The first two main COG functional categories of DAPs in both alfalfa varieties after drought stress were 'Translation, ribosomal structure and biogenesis' and 'Posttranslational modification, protein turnover, chaperones'. According to KEGG database, the DAPs of the two alfalfa cultivars after drought treatment were differentially enriched in different biological pathways. The DAPs from Algonquin were enriched in 'photosynthesis' and 'ribosome'. The pathways of 'linoleic acid metabolism', 'protein processing in endoplasmic reticulum' and 'RNA transport' in Longdong were significantly enriched. Finally, we found significant differences in DAP enrichment and expression patterns between Longdong and Algonquin in glycolysis/glycogenesis, TCA cycle, photosynthesis, protein biosynthesis, flavonoid and isoflavonoid biosynthesis, and plant-pathogen interaction pathway after drought treatment.

CONCLUSIONS

The differences of DAPs involved in various metabolic pathways may explain the differences in the resistance of the two varieties to drought stress. These DAPs can be used as candidate proteins for molecular breeding of alfalfa to cultivate new germplasm with more drought tolerance to adapt to unfavorable environments.

Analysis of N6-methyladenosine reveals a new important mechanism regulating the salt tolerance of sugar beet (Beta vulgaris)

Salinity is an important environmental factor in crop growth and development. N6-methyladenosine (m6A) is an essential epigenetic modification that regulates plant-environment interaction. Sugar beet is a major sugar-yielding crop that has a certain tolerance to salt, but the dynamic response elicited by the m6A modification of transcripts under salt stress remains unknown. In this study, sugar beet was exposed to 300 mM NaCl to investigate its physiological response to high salinity and transcriptome-wide m6A modification profile. After the salt treatment, 7737 significantly modified m6A sites and 4981 differentially expressed genes (DEGs) were identified. Among the 312 m6A-modified DEGs, 113 hypomethylated DEGs were up-regulated and 99 hypermethylated DEGs were down-regulated, indicating a negative correlation between m6A modification and gene expression. Well-known salt tolerance genes (e.g., sodium/hydrogen exchanger 1, choline monooxygenase, and nucleoredoxin 2) and phospholipid signaling pathway genes (phosphoinositol-specific phospholipase C, phospholipase D, diacylglycerol kinase 1, etc.) were also among the m6A-modified genes. Further analysis showed that m6A modification may regulate salt-tolerant related gene expression by controlling mRNA stability. Therefore, changes in m6A modification may negatively regulate the expression of the salt-resistant genes in sugar beet, at least in part by modulating the stability of the mRNA via demethylase BvAlkbh10B. These findings could provide a better understanding of the epigenetic mechanisms of salt tolerance in sugar beets and uncover new candidate genes for improving the production of sugar beets planted in high-salinity soil.

Unique Features of the m6A Methylome and Its Response to Salt Stress in the Roots of Sugar Beet (Beta vulgaris)

Salt is one of the most important environmental factors in crop growth and development. N⁶-methyladenosine (m⁶A) is an epigenetic modification that regulates plant-environment interaction at transcriptional and translational levels. Sugar beet is a salt-tolerant sugar-yielding crop, but how m⁶A modification affects its response to salt stress remains unknown. In this study, m⁶A-seq was used to explore the role of m⁶A modification in response to salt stress in sugar beet (Beta vulgaris). Transcriptome-wide m⁶A methylation profiles and physiological responses to high salinity were investigated in beet roots. After treatment with 300 mM NaCl, the activities of peroxidase and catalase, the root activity, and the contents of Na⁺, K⁺, and Ca²⁺ in the roots were significantly affected by salt stress. Compared with the control plants, 6904 differentially expressed genes (DEGs) and 566 differentially methylated peaks (DMPs) were identified. Association analysis revealed that 243 DEGs contained DMP, and 80% of these DEGs had expression patterns that were negatively correlated with the extent of m⁶A modification. Further analysis verified that m⁶A methylation may regulate the expression of some genes by controlling their mRNA stability. Functional analysis revealed that m⁶A modifications primarily affect the expression of genes involved in energy metabolism, transport, signal transduction, transcription factors, and cell wall organization. This study provides evidence that a post-transcriptional regulatory mechanism mediates gene expression during salt stress by affecting the stability of mRNA in the root.

Transcriptome, proteome and functional characterization reveals salt stress tolerance mechanisms in upland cotton (Gossypium hirsutum L.)

Uncovering the underlying mechanism of salt tolerance is important to breed cotton varieties with improved salt tolerance. In this study, transcriptome and proteome sequencing were performed on upland cotton (Gossypium hirsutum L.) variety under salt stress, and integrated analysis was carried out to exploit salt-tolerance genes in cotton. Enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed on differentially expressed genes (DEGs) obtained from transcriptome and proteome sequencing. GO enrichment was carried out mainly in the cell membrane, organelle, cellular process, metabolic process, and stress response. The expression of 23,981 genes was changed in physiological and biochemical processes such as cell metabolism. The metabolic pathways obtained by KEGG enrichment included glycerolipid metabolism, sesquiterpene and triterpenoid biosynthesis, flavonoid production, and plant hormone signal transduction. Combined transcriptome and proteome analysis to screen and annotate DEGs yielded 24 candidate genes with significant differential expression. The quantitative real-time polymerase chain reaction (qRT-PCR) validation of the candidate genes showed that two genes (Gh_D11G0978 and Gh_D10G0907) responded significantly to the induction of NaCl, and these two genes were further selected as target genes for gene cloning and functional validation through virus-induced gene silencing (VIGS). The silenced plants exhibited early wilting with a greater degree of salt damage under salt treatment. Moreover, they showed higher levels of reactive oxygen species (ROS) than the control. Therefore, we can infer that these two genes have a pivotal role in the response to salt stress in upland cotton. The findings in this research will facilitate the breeding of salt tolerance cotton varieties that can be grown on saline alkaline lands.

Alteration of proteome in germinating seedlings of piegonpea (Cajanus cajan) after salt stress

Pigeonpea (Cajanus cajan) is an important crop in semi-arid regions and a significant source of dietary proteins in India. The plant is sensitive to salinity stress, which adversely affects its productivity. Based on the dosage-dependent influence of salinity stress on the growth and ion contents in the young seedlings of pigeonpea, a comparative proteome analysis of control and salt stressed (150 mM NaCl) plants was conducted using 7 days-old seedlings. Among various amino acids, serine, aspartate and asparagine were the amino acids that showed increment in the root, whereas serine, aspartate and phenylalanine showed an upward trend in shoots under salt stress. Furthermore, a label-free and gel-free comparative Q-Tof, Liquid Chromatography-Mass spectrometry (LC-MS) revealed total of 118 differentially abundant proteins in roots and shoots with and without salt stress conditions. Proteins related to DNA-binding with one finger (Dof) transcription factor family and glycine betaine (GB) biosynthesis were differentially expressed in the shoot and root of the salinity-stressed seedlings. Exogenous application of choline on GB accumulation under salt stress showed the increase of GB pathway in C. cajan. Gene expression analysis for differentially abundant proteins revealed the higher induction of ethanolamine kinase (CcEthKin), choline-phosphate cytidylyltransferase 1-like (CcChoPh), serine hydroxymethyltransferase (CcSHMT) and Dof protein (CcDof29). The results indicate the importance of, choline precursor, serine biosynthetic pathways and glycine betaine synthesis in salinity stress tolerance. The glycine betaine protects plant from cellular damages and acts as osmoticum under stress condition. Protein interaction network (PIN) analysis demonstrated that 61% of the differentially expressed proteins exhibited positive interactions and 10% of them formed the center of the PIN. Further, The PIN analysis also highlighted the potential roles of the cytochrome c oxidases in sensing and signaling cascades governing salinity stress responses in pigeonpea.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01116-w.

Salt and Drought Stress Responses in Cultivated Beets (Beta vulgaris L.) and Wild Beet (Beta maritima L.)

Cultivated beets, including leaf beets, garden beets, fodder beets, and sugar beets, which belong to the species Beta vulgaris L., are economically important edible crops that have been originated from a halophytic wild ancestor, Beta maritima L. (sea beet or wild beet). Salt and drought are major abiotic stresses, which limit crop growth and production and have been most studied in beets compared to other environmental stresses. Characteristically, beets are salt- and drought-tolerant crops; however, prolonged and persistent exposure to salt and drought stress results in a significant drop in beet productivity and yield. Hence, to harness the best benefits of beet cultivation, knowledge of stress-coping strategies, and stress-tolerant beet varieties, are prerequisites. In the current review, we have summarized morpho-physiological, biochemical, and molecular responses of sugar beet, fodder beet, red beet, chard (B. vulgaris L.), and their ancestor, wild beet (B. maritima L.) under salt and drought stresses. We have also described the beet genes and noncoding RNAs previously reported for their roles in salt and drought response/tolerance. The plant biologists and breeders can potentiate the utilization of these resources as prospective targets for developing crops with abiotic stress tolerance.

Growth, Stoichiometry, and Palatability of Suaeda salsa From Different Habitats Are Demonstrated by Differentially Expressed Proteins and Their Enriched Pathways

Suaeda salsa (L.) Pall., a medicinal and edible plant, has green and red-violet ecotypes that exhibit different phenotypes, tastes, and growth characteristics. However, few studies have focused on these differences from the aspect of differentially expressed proteins under the conditions of different habitats in the field. In this study, two ecotypes of S. salsa from the intertidal (control) and supratidal (treatment) habitats of the Yellow River Delta were selected. A total of 30 individual leaves were mixed into six samples (three biological replicates for each) and subjected to protein extraction by using tandem mass tag-labeled quantitative proteomic technology. A total of 4771 proteins were quantitated. They included 317 differentially expressed proteins (2.0-fold change, p < 0.05), among which 143 were upregulated and the remaining 174 were downregulated. These differentially expressed proteins mainly participated in biological processes, such as response to stimulus, stress, and biotic stimulus; in molecular functions, such as methyltransferase activity, transferase activity, one-C group transfer, and tetrapyrrole binding; and in cell components, such as non-membrane-bound organelles, intracellular non-membrane-bound organelles, chromosomes, and photosystems. The differentially expressed proteins were mainly enriched in eight pathways, among which the ribosome, phenylpropanoid biosynthesis, and photosynthesis pathways had higher protein numbers than the other pathways. The upregulation of differentially expressed proteins related to the ribosome and photosynthesis increased the relative growth rate and reduced the N:P ratio of S. salsa from the supratidal habitat, thereby improving its palatability. By contrast, most of the differentially expressed proteins involved in phenylpropanoid biosynthesis were downregulated in S. salsa from the intertidal habitat. This result indicated that S. salsa from the intertidal habitat might accumulate flavonoids, lignin, and other secondary metabolites in its leaves that confer a bitter taste. However, these secondary metabolites might increase the medicinal value of S. salsa from the intertidal habitat. This work could provide a theoretical basis and data support for the sustainable and high-value utilization of medicinal and edible plants from coastal wetlands.

Whole-Transcriptome RNA Sequencing Reveals the Global Molecular Responses and CeRNA Regulatory Network of mRNAs, lncRNAs, miRNAs and circRNAs in Response to Salt Stress in Sugar Beet (Beta vulgaris)

Sugar beet is an important sugar-yielding crop with some tolerance to salt, but the mechanistic basis of this tolerance is not known. In the present study, we have used whole-transcriptome RNA-seq and degradome sequencing in response to salt stress to uncover differentially expressed (DE) mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in both leaves and roots. A competitive endogenous RNA (ceRNA) network was constructed with the predicted DE pairs, which revealed regulatory roles under salt stress. A functional analysis suggests that ceRNAs are implicated in copper redistribution, plasma membrane permeability, glycometabolism and energy metabolism, NAC transcription factor and the phosphoinositol signaling system. Overall, we conducted for the first time a full transcriptomic analysis of sugar beet under salt stress that involves a potential ceRNA network, thus providing a basis to study the potential functions of lncRNAs/circRNAs.