GmSK1, an SKP1 homologue in soybean, is involved in the tolerance to salt and drought

The ubiquitin-proteasome system in the plant response to abiotic stress: Potential role in crop resilience improvement

The post-translational modification (PTM) of proteins by ubiquitination modulates many physiological processes in plants. As the major protein degradation pathway in plants, the ubiquitin-proteasome system (UPS) is considered a promising target for improving crop tolerance drought, high salinity, extreme temperatures, and other abiotic stressors. The UPS also participates in abiotic stress-related abscisic acid (ABA) signaling. E3 ligases are core components of the UPS-mediated modification process due to their substrate specificity. In this review, we focus on the abiotic stress-associated regulatory mechanisms and functions of different UPS components, emphasizing the participation of E3 ubiquitin ligases. We also summarize and discuss UPS-mediated modulation of ABA signaling. In particular, we focus our review on recent research into the UPS-mediated modulation of the abiotic stress response in major crop plants. We propose that altering the ubiquitination site of the substrate or the substrate-specificity of E3 ligase using genome editing technology such as CRISPR/Cas9 may improve the resistance of crop plants to adverse environmental conditions. Such a strategy will require continued research into the role of the UPS in mediating the abiotic stress response in plants.

Identification of QTNs, QTN-by-environment interactions, and their candidate genes for salt tolerance related traits in soybean

BACKGROUND

Salt stress significantly reduces soybean yield. To improve salt tolerance in soybean, it is important to mine the genes associated with salt tolerance traits.

RESULTS

Salt tolerance traits of 286 soybean accessions were measured four times between 2009 and 2015. The results were associated with 740,754 single nucleotide polymorphisms (SNPs) to identify quantitative trait nucleotides (QTNs) and QTN-by-environment interactions (QEIs) using three-variance-component multi-locus random-SNP-effect mixed linear model (3VmrMLM). As a result, eight salt tolerance genes (GmCHX1, GsPRX9, Gm5PTase8, GmWRKY, GmCHX20a, GmNHX1, GmSK1, and GmLEA2-1) near 179 significant and 79 suggested QTNs and two salt tolerance genes (GmWRKY49 and GmSK1) near 45 significant and 14 suggested QEIs were associated with salt tolerance index traits in previous studies. Six candidate genes and three gene-by-environment interactions (GEIs) were predicted to be associated with these index traits. Analysis of four salt tolerance related traits under control and salt treatments revealed six genes associated with salt tolerance (GmHDA13, GmPHO1, GmERF5, GmNAC06, GmbZIP132, and GmHsp90s) around 166 QEIs were verified in previous studies. Five candidate GEIs were confirmed to be associated with salt stress by at least one haplotype analysis. The elite molecular modules of seven candidate genes with selection signs were extracted from wild soybean, and these genes could be applied to soybean molecular breeding. Two of these genes, Glyma06g04840 and Glyma07g18150, were confirmed by qRT-PCR and are expected to be key players in responding to salt stress.

CONCLUSIONS

Around the QTNs and QEIs identified in this study, 16 known genes, 6 candidate genes, and 8 candidate GEIs were found to be associated with soybean salt tolerance, of which Glyma07g18150 was further confirmed by qRT-PCR.

Identification and Expression Analysis of the SKP1-Like Gene Family under Phytohormone and Abiotic Stresses in Apple (Malus domestica)

Ubiquitination participates in plant hormone signaling and stress response to adversity. SKP1-Like, a core component of the SCF (Skp1-Cullin-F-box) complex, is the final step in catalyzing the ubiquitin-mediated protein degradation pathway. However, the SKP1-Like gene family has not been well characterized in response to apple abiotic stresses and hormonal treatments. This study revealed that 17 MdSKP1-Like gene family members with the conserved domain of SKP1 were identified in apples and were unevenly distributed on eight chromosomes. The MdSKP1-Like genes located on chromosomes 1, 10, and 15 were highly homologous. The MdSKP1-like genes were divided into three subfamilies according to the evolutionary affinities of monocotyledons and dicotyledons. MdSKP1-like members of the same group or subfamily show some similarity in gene structure and conserved motifs. The predicted results of protein interactions showed that members of the MdSKP1-like family have strong interactions with members of the F-Box family of proteins. A selection pressure analysis showed that MdSKP1-Like genes were in purifying selection. A chip data analysis showed that MdSKP1-like14 and MdSKP1-like15 were higher in flowers, whereas MdSKP1-like3 was higher in fruits. The upstream cis-elements of MdSKP1-Like genes contained a variety of elements related to light regulation, drought, low temperature, and many hormone response elements, etc. Meanwhile, qRT-PCR also confirmed that the MdSKP1-Like gene is indeed involved in the response of the apple to hormonal and abiotic stress treatments. This research provides evidence for regulating MdSKP1-Like gene expression in response to hormonal and abiotic stresses to improve apple stress resistance.

Twenty years of mining salt tolerance genes in soybean

Current combined challenges of rising food demand, climate change and farmland degradation exert enormous pressure on agricultural production. Worldwide soil salinization, in particular, necessitates the development of salt-tolerant crops. Soybean, being a globally important produce, has its genetic resources increasingly examined to facilitate crop improvement based on functional genomics. In response to the multifaceted physiological challenge that salt stress imposes, soybean has evolved an array of defences against salinity. These include maintaining cell homeostasis by ion transportation, osmoregulation, and restoring oxidative balance. Other adaptations include cell wall alterations, transcriptomic reprogramming, and efficient signal transduction for detecting and responding to salt stress. Here, we reviewed functionally verified genes that underly different salt tolerance mechanisms employed by soybean in the past two decades, and discussed the strategy in selecting salt tolerance genes for crop improvement. Future studies could adopt an integrated multi-omic approach in characterizing soybean salt tolerance adaptations and put our existing knowledge into practice via omic-assisted breeding and gene editing. This review serves as a guide and inspiration for crop developers in enhancing soybean tolerance against abiotic stresses, thereby fulfilling the role of science in solving real-life problems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01383-3.

Role of F-box E3-ubiquitin ligases in plant development and stress responses

KEY MESSAGE

F-box E3-ubiquitin ligases regulate critical biological processes in plant development and stress responses. Future research could elucidate why and how plants have acquired a large number of F-box genes. The ubiquitin-proteasome system (UPS) is a predominant regulatory mechanism employed by plants to maintain the protein turnover in the cells and involves the interplay of three classes of enzymes, E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 ligases. The diverse and most prominent protein family among eukaryotes, F-box proteins, are a vital component of the multi-subunit SCF (Skp1-Cullin 1-F-box) complex among E3 ligases. Several F-box proteins with multifarious functions in different plant systems have evolved rapidly over time within closely related species, but only a small part has been characterized. We need to advance our understanding of substrate-recognition regulation and the involvement of F-box proteins in biological processes and environmental adaptation. This review presents a background of E3 ligases with particular emphasis on the F-box proteins, their structural assembly, and their mechanism of action during substrate recognition. We discuss how the F-box proteins regulate and participate in the signaling mechanisms of plant development and environmental responses. We highlight an urgent need for research on the molecular basis of the F-box E3-ubiquitin ligases in plant physiology, systems biology, and biotechnology. Further, the developments and outlooks of the potential technologies targeting the E3-ubiquitin ligases for developing crop improvement strategies have been discussed.

The soybean ubiquitin-proteasome system: Current knowledge and future perspective

Increasing soybean [Glycine max (L.) Merr.] yield has become a worldwide scientific problem in the world. Many studies have shown that ubiquitination plays a key role in stress response and yield formation. In the UniProtKB database, 2,429 ubiquitin-related proteins were predicted in soybean, however, <20 were studied. One key way to address this lack of progress in increasing soybean yield will be a deeper understanding of the ubiquitin-proteasome system (UPS) in soybean. In this review, we summarized the current knowledge about soybean ubiquitin-related proteins and discussed the method of combining phenotype, mutant library, transgenic system, genomics, and proteomics approaches to facilitate the exploration of the soybean UPS. We also proposed the strategy of applying the UPS in soybean improvement based on related studies in model plants. Our review will be helpful for soybean scientists to learn current research progress of the soybean UPS and further lay a theoretical reference for the molecular improvement of soybean in future research by use of this knowledge.

Drought and Heat Stress in Cool-Season Food Legumes in Sub-Tropical Regions: Consequences, Adaptation, and Mitigation Strategies

Drought and heat stress are two major abiotic stresses that challenge the sustainability of agriculture to a larger extend. The changing and unpredictable climate further aggravates the efforts made by researchers as well as farmers. The stresses during the terminal stage of cool-season food legumes may affect numerous physiological and biochemical reactions that may result in poor yield. The plants possess a good number of adaptative and avoiding mechanisms to sustain the adverse situation. The various agronomic and breeding approaches may help in stress-induced alteration. The physiological and biochemical response of crops to any adverse situation is very important to understand to develop mechanisms and approaches for tolerance in plants. Agronomic approaches like altering the planting time, seed priming, foliar application of various macro and micro nutrients, and the application of rhizobacteria may help in mitigating the adverse effect of heat and drought stress to some extent. Breeding approaches like trait-based selection, inheritance studies of marker-based selection, genetic approaches using the transcriptome and metabolome may further pave the way to select and develop crops with better heat and drought stress adaptation and mitigation.

Physiological, biochemical, and transcriptional regulation in a leguminous forage Trifolium pratense L. responding to silver ions

Trifolium pratense L. (red clover) is an important leguminous crop with great potential for Ag-contaminated environment remediation. Whereas, the molecular mechanisms of Ag tolerance in red clover are largely unknown. Red clover seedlings were used for physiological and transcriptomic investigation under 0, 20, 50, and 100 mg/L Ag⁺ stress in our research to reveal potential molecular resistance mechanism. Research showed that red clover possessed fairly strong Ag absorbance capacity, the Ag level reached 0.14 and 2.35 mg/g·FW in the leaves and roots under 100 mg/L AgNO₃ stress condition. Root fresh weight, root dry weight, root water content, and photosynthetic pigments contents were significantly decreased with elevating AgNO₃ concentration. Obvious withered plant tissue, microstructure disorder, and disrupted organelles were observed. In vitro evaluations (e.g., PI and DCFH-DA staining) represented that AgNO₃ at high concentration (100 mg/L) exhibited obvious inhibition on cell viability, which was due possibly to the induction of reactive oxygen species (ROS) accumulation. A total of 44643 differentially expressed genes (DEGs) were identified under Ag stress, covering 27155 upregulated and 17488 downregulated genes. 12 stress-responsive DEGs was authenticated utilizing real-time quantitative PCR (qRT-PCR). Gene ontology (GO) analysis revealed that the DEGs were mostly related to metal ion binding (molecular function), nucleus (cellular component), and defense response (biological process). Involved DEGs in sequence-specific DNA binding transcription factor activity, response to various hormones (e.g., abscisic acid, IAA/Auxin, salicylic acid, and etc), calcium signal transduction, and protein ubiquitination were concluded to play crucial roles in Ag tolerance of red clover. On the other hand, Kyoto Encyclopedia of Genes and Genomes (KEGG) database annotated several stress responsive pathways such as plant-pathogen interaction, phenylpropanoid biosynthesis, ubiquitin mediated proteolysis, hormone signal transduction, and autophagy. Several down-regulated genes (e.g., RSF2, RCD1, DOX1, and etc) were identified indicating possible metabolic disturbance. Besides, protein-protein interaction network (PPI) identified several pivotal genes such as ribosomal proteins, TIR, and ZAT.

Bulk RNA-Seq analysis to dissect the regulation of stigma position in tomato

Transcriptomic analysis of tomato genotypes contrasting for stigma position suggests that stigma insertion occurred by the disruption of a process that finds a parallel in Arabidopsis gynoecium development. Domestication of cultivated tomato (Solanum lycopersicum L.) included the transition from allogamy to autogamy that occurred through the loss of self-incompatibilty and the retraction of the stigma within the antheridial cone. Although the inserted stigma is an established phenotype in modern tomatoes, an exserted stigma is still present in several landraces or vintage varieties. Moreover, exsertion of the stigma is a frequent response to high temperature stress and, being a cause of reduced fertility, a trait of increasing importance. Few QTLs for stigma position have been described and only one of the underlying genes identified. To gain insights on genes involved in stigma position in tomato, a bulk RNA sequencing (RNA-Seq) approach was adopted, using two groups of contrasting genotypes. Phenotypic analysis confirmed the extent and the stability of stigma position in the selected genotypes, whereas they were highly heterogeneous for other reproductive and productive traits. The RNA-Seq analysis yielded 801 differentially expressed genes (DEGs), 566 up-regulated and 235 down-regulated in the genotypes with exserted stigma. Validation by quantitative PCR indicated a high reliability of the RNA-Seq data. Up-regulated DEGs were enriched for genes involved in the cell wall metabolism, lipid transport, auxin response and flavonoid biosynthesis. Down-regulated DEGs were enriched for genes involved in translation. Validation of selected genes on pistil tissue of the 26 single genotypes revealed that differences between bulks could both be due to a general trend of the bulk or to the behaviour of single genotypes. Novel candidate genes potentially involved in the control of stigma position in tomato are discussed.

SKP1-like protein, CrSKP1-e, interacts with pollen-specific F-box proteins and assembles into SCF-type E3 complex in 'Wuzishatangju' (Citrus reticulata Blanco) pollen

S-ribonuclease (S-RNase)-based self-incompatibility (SI) mechanisms have been extensively studied in Solanaceae, Rosaceae and Plantaginaceae. S-RNase-based SI is controlled by two closely related genes, S-RNase and S-locus F-box (SLF), located at a polymorphic S-locus. In the SI system, the SCF-type (SKP1-CUL1-F-box-RBX1) complex functions as an E3 ubiquitin ligase complex for ubiquitination of non-self S-RNase. Pummelo (Citrus grandis) and several mandarin cultivars are suggested to utilize an S-RNase-based SI system. However, the molecular mechanism of the non-S-factors involved in the SI reaction is not straightforward in Citrus. To investigate the SCF-type E3 complex responsible for the SI reaction in mandarin, SLF, SKP1-like and CUL1 candidates potentially involved in the SI reaction of ‘Wuzishatangju’ (Citrus reticulata Blanco) were identified based on the genome-wide identification and expression analyses. Sixteen pollen-specific F-box genes (CrFBX1-CrFBX16), one pollen-specific SKP1-like gene (CrSKP1-e) and two CUL1 genes (CrCUL1A and CrCUL1B) were identified and cloned from ‘Wuzishatangju’. Yeast two-hybrid (Y2H) and in vitro binding assays showed that five CrFBX proteins could bind to CrSKP1-e, which is an ortholog of SSK1 (SLF-interacting-SKP1-like), a non-S-factor responsible for the SI reaction. Luciferase complementation imaging (LCI) and in vitro binding assays also showed that CrSKP1-e interacts with the N-terminal region of both CrCUL1A and CrCUL1B. These results indicate that CrSKP1-e may serve as a functional member of the SCF-type E3 ubiquitin ligase complex in ‘Wuzishatangju’.

Raman Spectroscopic and Chemometric Investigation of Lipid-Protein Ratio Contents of Soybean Mutants

Seeds belonging to fourth generation mutants (M4) of Ataem-7 cultivar (A7) variety and S04-05 (S) breeding line salt-tolerant soybeans were investigated by Raman spectroscopy, complemented by chemometrics methods, in order to evaluate changes induced by mutations in the relative lipid-protein contents, and to find fast, efficient strategies for discrimination of the mutants and the control groups based on their Raman spectra. It was concluded that gamma irradiation caused an increase in the lipid to protein ratio of the studied Ataem-7 variety mutants, while it led to a decrease of this ratio in the investigated S04-05 breeding line mutants. These results were found to be in agreement with data obtained by reflectance spectrum analysis of the seeds in the full ultraviolet to near-infrared spectral region and suggest the possibility of developing strategies where gamma irradiation can be used as a tool to improve mutant soybean plants targeted to different applications, either enriched in proteins or in lipids. Ward's clustering and principal component analysis showed a clear discrimination between mutants and controls and, in the case of the studied S-type species, discrimination between the different mutants. The grouping scheme is also found to be in agreement with the compositional information extracted from the analysis of the lipid-protein contents of the different samples.

A Glycine max sodium/hydrogen exchanger enhances salt tolerance through maintaining higher Na+ efflux rate and K+/Na+ ratio in Arabidopsis

BACKGROUND

Soybean (Glycine max (L.)) is one the most important oil-yielding cash crops. However, the soybean production has been seriously restricted by salinization. It is therefore crucial to identify salt tolerance-related genes and reveal molecular mechanisms underlying salt tolerance in soybean crops. A better understanding of how plants resist salt stress provides insights in improving existing soybean varieties as well as cultivating novel salt tolerant varieties. In this study, the biological function of GmNHX1, a NHX-like gene, and the molecular basis underlying GmNHX1-mediated salt stress resistance have been revealed.

RESULTS

We found that the transcription level of GmNHX1 was up-regulated under salt stress condition in soybean, reaching its peak at 24 h after salt treatment. By employing the virus-induced gene silencing technique (VIGS), we also found that soybean plants became more susceptible to salt stress after silencing GmNHX1 than wild-type and more silenced plants wilted than wild-type under salt treatment. Furthermore, Arabidopsis thaliana expressing GmNHX1 grew taller and generated more rosette leaves under salt stress condition compared to wild-type. Exogenous expression of GmNHX1 resulted in an increase of Na+ transportation to leaves along with a reduction of Na+ absorption in roots, and the consequent maintenance of a high K+/Na+ ratio under salt stress condition. GmNHX1-GFP-transformed onion bulb endothelium cells showed fluorescent pattern in which GFP fluorescence signals enriched in vacuolar membranes. Using the non-invasive micro-test technique (NMT), we found that the Na+ efflux rate of both wild-type and transformed plants after salt treatment were significantly higher than that of before salt treatment. Additionally, the Na+ efflux rate of transformed plants after salt treatment were significantly higher than that of wild-type. Meanwhile, the transcription levels of three osmotic stress-related genes, SKOR, SOS1 and AKT1 were all up-regulated in GmNHX1-expressing plants under salt stress condition.

CONCLUSION

Vacuolar membrane-localized GmNHX1 enhances plant salt tolerance through maintaining a high K+/Na+ ratio along with inducing the expression of SKOR, SOS1 and AKT1. Our findings provide molecular insights on the roles of GmNHX1 and similar sodium/hydrogen exchangers in regulating salt tolerance.

Functional Analysis of Pepper F-box Protein CaDIF1 and Its Interacting Partner CaDIS1: Modulation of ABA Signaling and Drought Stress Response

Plant adaptive responses to environmental stress are coordinated by inhibition of plant growth and development. Abscisic acid (ABA) is a major phytohormone that regulates the stress response, and its sensitivity determines stress tolerance levels. In this study, we report the identification and functional role of a novel F-box protein, CaDIF1 (Capsicum annuum Drought-Induced F-box Protein 1). The expression of CaDIF1 in pepper leaves was induced by ABA, drought, H₂O₂, and NaCl treatments. In comparison with wild-type pepper plants, CaDIF1-silenced pepper plants exhibited a drought-sensitive phenotype, whereas CaDIF1-overexpressing (OX) plants exhibited ABA-sensitive and drought-tolerant phenotypes. Using a yeast two-hybrid assay, we identified CaDIS1 (C. annuum DIF1-Interacting SKP 1), which interacts with CaDIF1 in the cytoplasm and nucleus. Consistent with CaDIF1-silenced pepper plants, CaDIS1-silenced pepper plants displayed ABA insensitivity and reduced drought tolerance, and these were characterized by larger stomatal apertures and greater transpirational water loss. Taken together, our results indicate that CaDIF1 and its interacting partner CaDIS1 synergistically regulate the ABA-dependent defence signaling response to drought stress.

Transcript expression profiling in two contrasting cultivars and molecular cloning of a SKP-1 like gene, a component of SCF-ubiquitin proteasome system from mungbean Vigna radiate L

Protein degradation and turnover under various environmental stresses is basically regulated by ubiquitin-proteasome system (UPS), of which SKP1 is a very essential component. Isolation and cloning of an identified potential stress responsive candidate gene SKP1, was successfully done for the first time to fathom the role of SKP1 in drought tolerance at genetic level in drought tolerant mungbean cultivar Pratap, which was screened after a detailed physio-biochemical screening amongst seven popular mungbean cultivars. The cloned gene SKP1 (accession number KX881912) is 550 bp in length, encodes 114 amino acids. It shows high sequence homology with SKP1 from Zea mays (NP_001148633). The protein expression of isolated SKP1 was confirmed by GUS fused expression using a Histochemical assay under control as well as under drought stress. Further, up-regulation in relative expression level of SKP1 in different plant parts under drought stress confirmed its utility as a potential drought responsive candidate gene certainly demanding extensive genetic research for further incorporation in breeding programs. Moreover, the structure of VrSKP1 (Vigna radiata SKP1) has been modelled, validated and an Essential Dynamics (ED) was done on the Molecular Dynamics (MD) simulation trajectories for filtering large-scale concerted motions. Free-energy calculations on the ED revealed a complex free-energy landscape (FEL) implying the conformational diversity of the modelled VrSPK1 protein.

Research Progress and Perspective on Drought Stress in Legumes: A Review

Climate change, food shortage, water scarcity, and population growth are some of the threatening challenges being faced in today's world. Drought stress (DS) poses a constant challenge for agricultural crops and has been considered a severe constraint for global agricultural productivity; its intensity and severity are predicted to increase in the near future. Legumes demonstrate high sensitivity to DS, especially at vegetative and reproductive stages. They are mostly grown in the dry areas and are moderately drought tolerant, but severe DS leads to remarkable production losses. The most prominent effects of DS are reduced germination, stunted growth, serious damage to the photosynthetic apparatus, decrease in net photosynthesis, and a reduction in nutrient uptake. To curb the catastrophic effect of DS in legumes, it is imperative to understand its effects, mechanisms, and the agronomic and genetic basis of drought for sustainable management. This review highlights the impact of DS on legumes, mechanisms, and proposes appropriate management approaches to alleviate the severity of water stress. In our discussion, we outline the influence of water stress on physiological aspects (such as germination, photosynthesis, water and nutrient uptake), growth parameters and yield. Additionally, mechanisms, various management strategies, for instance, agronomic practices (planting time and geometry, nutrient management), plant growth-promoting Rhizobacteria and arbuscular mycorrhizal fungal inoculation, quantitative trait loci (QTLs), functional genomics and advanced strategies (CRISPR-Cas9) are also critically discussed. We propose that the integration of several approaches such as agronomic and biotechnological strategies as well as advanced genome editing tools is needed to develop drought-tolerant legume cultivars.

Grain Legumes and Fear of Salt Stress: Focus on Mechanisms and Management Strategies

Salinity is an ever-present major constraint and a major threat to legume crops, particularly in areas with irrigated agriculture. Legumes demonstrate high sensitivity, especially during vegetative and reproductive phases. This review gives an overview of legumes sensitivity to salt stress (SS) and mechanisms to cope with salinity stress under unfavorable conditions. It also focuses on the promising management approaches, i.e., agronomic practices, breeding approaches, and genome editing techniques to improve performance of legumes under SS. Now, the onus is on researchers to comprehend the plants physiological and molecular mechanisms, in addition to various responses as part of their stress tolerance strategy. Due to their ability to fix biological nitrogen, high protein contents, dietary fiber, and essential mineral contents, legumes have become a fascinating group of plants. There is an immense need to develop SS tolerant legume varieties to meet growing demand of protein worldwide. This review covering crucial areas ranging from effects, mechanisms, and management strategies, may elucidate further the ways to develop SS-tolerant varieties and to produce legume crops in unfavorable environments.

Abiotic Stresses: General Defenses of Land Plants and Chances for Engineering Multistress Tolerance

Abiotic stresses, such as low or high temperature, deficient or excessive water, high salinity, heavy metals, and ultraviolet radiation, are hostile to plant growth and development, leading to great crop yield penalty worldwide. It is getting imperative to equip crops with multistress tolerance to relieve the pressure of environmental changes and to meet the demand of population growth, as different abiotic stresses usually arise together in the field. The feasibility is raised as land plants actually have established more generalized defenses against abiotic stresses, including the cuticle outside plants, together with unsaturated fatty acids, reactive species scavengers, molecular chaperones, and compatible solutes inside cells. In stress response, they are orchestrated by a complex regulatory network involving upstream signaling molecules including stress hormones, reactive oxygen species, gasotransmitters, polyamines, phytochromes, and calcium, as well as downstream gene regulation factors, particularly transcription factors. In this review, we aimed at presenting an overview of these defensive systems and the regulatory network, with an eye to their practical potential via genetic engineering and/or exogenous application.