SCF E3 ligase PP2-B11 plays a positive role in response to salt stress in Arabidopsis

Comparative RNA-seq analysis of Arabidopsis thaliana response to AtPep1 and flg22, reveals the identification of PP2-B13 and ACLP1 as new members in pattern-triggered immunity

In this research, a high-throughput RNA sequencing-based transcriptome analysis technique (RNA-Seq) was used to evaluate differentially expressed genes (DEGs) in the wild type Arabidopsis seedlings in response to AtPep1, a well-known peptide representing an endogenous damage-associated molecular pattern (DAMP), and flg22, a well-known microbe-associated molecular pattern (MAMP). We compared and dissected the global transcriptional landscape of Arabidopsis thaliana in response to AtPep1 and flg22 and could identify shared and unique DEGs in response to these elicitors. We found that while a remarkable number of flg22 up-regulated genes were also induced by AtPep1, 256 genes were exclusively up-regulated in response to flg22, and 328 were exclusively up-regulated in response to AtPep1. Furthermore, among down-regulated DEGs upon flg22 treatment, 107 genes were exclusively down-regulated by flg22 treatment, while 411 genes were exclusively down-regulated by AtPep1. We found a number of hitherto overlooked genes to be induced upon treatment with either flg22 or with AtPep1, indicating their possible involvement general pathways in innate immunity. Here, we characterized two of them, namely PP2-B13 and ACLP1. pp2-b13 and aclp1 mutants showed increased susceptibility to infection by the virulent pathogen Pseudomonas syringae DC3000 and its mutant Pst DC3000 hrcC (lacking the type III secretion system), as evidenced by increased proliferation of the two pathogens in planta. Further, we present evidence that the aclp1 mutant is deficient in ethylene production upon flg22 treatment, while the pp2-b13 mutant is deficient in the production of reactive oxygen species (ROS). The results from this research provide new information for a better understanding of the immune system in Arabidopsis.

Overexpression of stress granule protein TZF1 enhances salt stress tolerance by targeting ACA11 mRNA for degradation in Arabidopsis

Tandem CCCH zinc finger (TZF) proteins play diverse roles in plant growth and stress response. Although as many as 11 TZF proteins have been identified in Arabidopsis, little is known about the mechanism by which TZF proteins select and regulate the target mRNAs. Here, we report that Arabidopsis TZF1 is a bona-fide stress granule protein. Ectopic expression of TZF1 (TZF1 OE), but not an mRNA binding-defective mutant (TZF1H186Y OE), enhances salt stress tolerance in Arabidopsis. RNA-seq analyses of NaCl-treated plants revealed that the down-regulated genes in TZF1 OE plants are enriched for functions in salt and oxidative stress responses. Because many of these down-regulated mRNAs contain AU- and/or U-rich elements (AREs and/or UREs) in their 3'-UTRs, we hypothesized that TZF1-ARE/URE interaction might contribute to the observed gene expression changes. Results from RNA immunoprecipitation-quantitative PCR analysis, gel-shift, and mRNA half-life assays indicate that TZF1 binds and triggers degradation of the autoinhibited Ca2+-ATPase 11 (ACA11) mRNA, which encodes a tonoplast-localized calcium pump that extrudes calcium and dampens signal transduction pathways necessary for salt stress tolerance. Furthermore, this salt stress-tolerance phenotype was recapitulated in aca11 null mutants. Collectively, our findings demonstrate that TZF1 binds and initiates degradation of specific mRNAs to enhance salt stress tolerance.

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.

GhFB15 is an F-box protein that modulates the response to salinity by regulating flavonoid biosynthesis

An exposure to extremely saline conditions can lead to significant oxidative damage in plants. Flavonoids, which are potent antioxidants, are critical for the scavenging of reactive oxygen species caused by abiotic stress. In the present study, the cotton F-box gene GhFB15 was isolated and characterized. The expression of GhFB15 was rapidly induced by salt as well as by exogenous hormones (ETH, MeJA, ABA, and GA). An analysis of subcellular localization revealed GhFB15 is mainly distributed in nuclei. Overexpression of GhFB15 adversely affected the salt tolerance of transgenic Arabidopsis plants as evidenced by decreased seed germination and seedling growth, whereas the silencing of GhFB15 improved the salt tolerance of cotton plants. Furthermore, we analyzed the gene expression profiles of VIGS-GhFB15 and TRV:00 plants. Many of the differentially expressed genes were associated with the flavonoid biosynthesis pathway. Moreover, lower flavonoid contents and higher levels of H2O2 and O2- were observed in the transgenic Arabidopsis plants. Conversely, the VIGS-GhFB15 cotton plants had relatively higher flavonoid contents, but lower H2O2 and O2- levels. These results suggest that GhFB15 negatively regulates salt tolerance, and silencing GhFB15 results in increased flavonoid accumulation and improved ROS scavenging.

Genome-wide analysis of long noncoding RNAs in response to salt stress in Nicotiana tabacum

BACKGROUND

Long noncoding RNAs (lncRNAs) have been shown to play important roles in the response of plants to various abiotic stresses, including drought, heat and salt stress. However, the identification and characterization of genome-wide salt-responsive lncRNAs in tobacco (Nicotiana tabacum L.) have been limited. Therefore, this study aimed to identify tobacco lncRNAs in roots and leaves in response to different durations of salt stress treatment.

RESULTS

A total of 5,831 lncRNAs were discovered, with 2,428 classified as differentially expressed lncRNAs (DElncRNAs) in response to salt stress. Among these, only 214 DElncRNAs were shared between the 2,147 DElncRNAs in roots and the 495 DElncRNAs in leaves. KEGG pathway enrichment analysis revealed that these DElncRNAs were primarily associated with pathways involved in starch and sucrose metabolism in roots and cysteine and methionine metabolism pathway in leaves. Furthermore, weighted gene co-expression network analysis (WGCNA) identified 15 co-expression modules, with four modules strongly linked to salt stress across different treatment durations (MEsalmon, MElightgreen, MEgreenyellow and MEdarkred). Additionally, an lncRNA-miRNA-mRNA network was constructed, incorporating several known salt-associated miRNAs such as miR156, miR169 and miR396.

CONCLUSIONS

This study enhances our understanding of the role of lncRNAs in the response of tobacco to salt stress. It provides valuable information on co-expression networks of lncRNA and mRNAs, as well as networks of lncRNAs-miRNAs-mRNAs. These findings identify important candidate lncRNAs that warrant further investigation in the study of plant-environment interactions.

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.

A systematic analysis of the phloem protein 2 (PP2) proteins in Gossypium hirsutum reveals that GhPP2-33 regulates salt tolerance

BACKGROUND

Phloem protein 2 (PP2) proteins play a vital role in the Phloem-based defense (PBD) and participate in many abiotic and biotic stress. However, research on PP2 proteins in cotton is still lacking.

RESULTS

A total of 25, 23, 43, and 47 PP2 genes were comprehensively identified and characterized in G.arboretum, G.raimondii, G.barbadense, and G.hirsutum. The whole genome duplication (WGD) and allopolyploidization events play essential roles in the expansion of PP2 genes. The promoter regions of GhPP2 genes contain many cis-acting elements related to abiotic stress and the weighted gene co-expression network analysis (WGCNA) analysis displayed that GhPP2s could be related to salt stress. The qRT-PCR assays further confirmed that GhPP2-33 could be dramatically upregulated during the salt treatment. And the virus-induced gene silencing (VIGS) experiment proved that the silencing of GhPP2-33 could decrease salt tolerance.

CONCLUSIONS

The results in this study not only offer new perspectives for understanding the evolution of PP2 genes in cotton but also further explore their function under salt stress.

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.

Genome-Wide Analysis and Characterization of Eggplant F-Box Gene Superfamily: Gene Evolution and Expression Analysis under Stress

F-box genes play an important role in plant growth and resistance to abiotic and biotic stresses. To date, systematic analysis of F-box genes and functional annotation in eggplant (Solanum melongena) is still limited. Here, we identified 389 F-box candidate genes in eggplant. The domain study of F-box candidate genes showed that the F-box domain is conserved, whereas the C-terminal domain is diverse. There are 376 SmFBX candidate genes distributed on 12 chromosomes. A collinearity analysis within the eggplant genome suggested that tandem duplication is the dominant form of F-box gene replication in eggplant. The collinearity analysis between eggplant and the three other species (Arabidopsis thaliana, rice and tomato) provides insight into the evolutionary characteristics of F-box candidate genes. In addition, we analyzed the expression of SmFBX candidate genes in different tissues under high temperature and bacterial wilt stress. The results identified several F-box candidate genes that potentially participate in eggplant heat tolerance and bacterial wilt resistance. Moreover, the yeast two-hybrid assay showed that several representative F-box candidate proteins interacted with representative Skp1 proteins. Overexpression of SmFBX131 and SmFBX230 in tobacco increased resistance to bacterial wilt. Overall, these results provide critical insights into the functional analysis of the F-box gene superfamily in eggplant and provide potentially valuable targets for heat and bacterial resistance.

An F-box protein attenuates fungal xylanase-triggered immunity by destabilizing LRR-RLP NbEIX2 in a SOBIR1-dependent manner

Receptor-like proteins (RLPs) lacking the cytoplasmic kinase domain play crucial roles in plant growth, development and immunity. However, what remains largely elusive is whether RLP protein levels are fine-tuned by E3 ubiquitin ligases, which are employed by receptor-like kinases for signaling attenuation. Nicotiana benthamiana NbEIX2 is a leucine-rich repeat RLP (LRR-RLP) that mediates fungal xylanase-triggered immunity. Here we show that NbEIX2 associates with an F-box protein NbPFB1, which promotes NbEIX2 degradation likely by forming an SCF E3 ubiquitin ligase complex, and negatively regulates NbEIX2-mediated immune responses. NbEIX2 undergoes ubiquitination and proteasomal degradation in planta. Interestingly, NbEIX2 without its cytoplasmic tail is still associated with and destabilized by NbPFB1. In addition, NbPFB1 also associates with and destabilizes NbSOBIR1, a co-receptor of LRR-RLPs, and fails to promote NbEIX2 degradation in the sobir1 mutant. Our findings reveal a distinct model of NbEIX2 degradation, in which an F-box protein destabilizes NbEIX2 indirectly in a SOBIR1-dependent manner.

Genome-Wide Identification and Expression Patterns of the F-box Family in Poplar under Salt Stress

The F-box family exists in a wide variety of plants and plays an extremely important role in plant growth, development and stress responses. However, systematic studies of F-box family have not been reported in populus trichocarpa. In the present study, 245 PtrFBX proteins in total were identified, and a phylogenetic tree was constructed on the basis of their C-terminal conserved domains, which was divided into 16 groups (A–P). F-box proteins were located in 19 chromosomes and six scaffolds, and segmental duplication was main force for the evolution of the F-box family in poplar. Collinearity analysis was conducted between poplar and other species including Arabidopsis thaliana, Glycine max, Anemone vitifolia Buch, Oryza sativa and Zea mays, which indicated that poplar has a relatively close relationship with G. max. The promoter regions of PtrFBX genes mainly contain two kinds of cis-elements, including hormone-responsive elements and stress-related elements. Transcriptome analysis indicated that there were 82 differentially expressed PtrFBX genes (DEGs), among which 64 DEGs were in the roots, 17 in the leaves and 26 in the stems. In addition, a co-expression network analysis of four representative PtrFBX genes indicated that their co-expression gene sets were mainly involved in abiotic stress responses and complex physiological processes. Using bioinformatic methods, we explored the structure, evolution and expression pattern of F-box genes in poplar, which provided clues to the molecular function of F-box family members and the screening of salt-tolerant PtrFBX genes.

Regulatory mechanisms behind the phenotypic plasticity associated with Setaria italica water deficit tolerance

Drought is one of the main environmental stresses that negatively impacts vegetative and reproductive yield. Water deficit responses are determined by the duration and intensity of the stress, which, together with plant genotype, will define the chances of plant survival. The metabolic adjustments in response to water deficit are complex and involve gene expression modulation regulated by DNA-binding proteins and epigenetic modifications. This last mechanism may also regulate the activity of transposable elements, which in turn impact the expression of nearby loci. Setaria italica plants submitted to five water deficit regimes were analyzed through a phenotypical approach, including growth, physiological, RNA-seq and sRNA-seq analyses. The results showed a progressive reduction in yield as a function of water deficit intensity associated with signaling pathway modulation and metabolic adjustments. We identified a group of loci that were consistently associated with drought responses, some of which were related to water deficit perception, signaling and regulation. Finally, an analysis of the transcriptome and sRNAome allowed us to identify genes putatively regulated by TE- and sRNA-related mechanisms and an intriguing positive correlation between transcript levels and sRNA accumulation in gene body regions. These findings shed light on the processes that allow S. italica to overcome drought and survive under water restrictive conditions.

An F-box protein from wheat, TaFBA-2A, negatively regulates JA biosynthesis and confers improved salt tolerance and increased JA responsiveness to transgenic rice plants

Soil salinity is a serious problem encountered by agriculture worldwide, which will lead to many harmful effects on plant growth, development, and even crop yield. F-box protein is the core subunit of the Skp1-Cullin-F-box (SCF) complex E3 ligase and plays crucial roles in regulating the growth, development, biotic & abiotic stresses, as well as hormone signaling pathway in plants. In this study, an FBA type F-box gene TaFBA-2A was isolated from wheat (Triticum aestivum L.). This study showed that TaFBA-2A could interact with TaSKP1, and TaOPR2, the crucial enzyme involving in jasmonic acid (JA) biosynthesis. TaFBA-2A negatively regulates JA biosynthesis, probably by mediating the degradation of TaOPR2 via the ubiquitin-26S proteasome pathway. Ectopic expression of TaFBA-2A improved the salt tolerance and increased the JA responsiveness of the transgenic rice lines. In addition, some agronomic traits closely related to crop yield were significantly enhanced in the rice lines ectopic expressing TaFBA-2A. The data obtained in this study shed light on the function and mechanisms of TaFBA-2A in JA biosynthesis and the responses to salt stress and JA treatment; this study also suggested that TaFBA-2A has the potential in improving the salt tolerance and crop yield of transgenic rice plants.

Construction of Chromosome Segment Substitution Lines and Inheritance of Seed-Pod Characteristics in Wild Soybean

Genetic populations provide the basis for genetic and genomic research, and chromosome segment substitution lines (CSSLs) are a powerful tool for the fine mapping of quantitative traits, new gene mining, and marker-assisted breeding. In this study, 213 CSSLs were obtained by self-crossing, backcrossing, and marker-assisted selection between cultivated soybean (Glycine max [L.] Merr.) variety Suinong14 (SN14) and wild soybean (Glycine soja Sieb. et Zucc.) ZYD00006. The genomes of these 213 CSSLs were resequenced and 580,524 single-nucleotide polymorphism markers were obtained, which were divided into 3,780 bin markers. The seed-pod-related traits were analyzed by quantitative trait locus (QTL) mapping using CSSLs. A total of 170 QTLs were detected, and 32 QTLs were detected stably for more than 2 years. Through epistasis analysis, 955 pairs of epistasis QTLs related to seed-pod traits were obtained. Furthermore, the hundred-seed weight QTL was finely mapped to the region of 64.4 Kb on chromosome 12, and Glyma.12G088900 was identified as a candidate gene. Taken together, a set of wild soybean CSSLs was constructed and upgraded by a resequencing technique. The seed-pod-related traits were studied by bin markers, and a candidate gene for the hundred-seed weight was finely mapped. Our results have revealed the CSSLs can be an effective tool for QTL mapping, epistatic effect analysis, and gene cloning.

The Characterization of the Phloem Protein 2 Gene Family Associated with Resistance to Sclerotinia sclerotiorum in Brassica napus

In plants, phloem is not only a vital structure that is used for nutrient transportation, but it is also the location of a response that defends against various stresses, named phloem-based defense (PBD). Phloem proteins (PP2s) are among the predominant proteins in phloem, indicating their potential functional role in PBD. Sclerotinia disease (SD), which is caused by the necrotrophic fungal pathogen S. sclerotiorum (Sclerotinia sclerotiorum), is a devastating disease that affects oil crops, especially Brassica napus (B. napus), mainly by blocking nutrition and water transportation through xylem and phloem. Presently, the role of PP2s in SD resistance is still largely estimated. Therefore, in this study, we identified 62 members of the PP2 gene family in the B. napus genome with an uneven distribution across the 19 chromosomes. A phylogenetic analysis classified the BnPP2s into four clusters (I-IV), with cluster I containing the most members (28 genes) as a consequence of its frequent genome segmental duplication. A comparison of the gene structures and conserved motifs suggested that BnPP2 genes were well conserved in clusters II to IV, but were variable in cluster I. Interestingly, the motifs in different clusters displayed unique features, such as motif 6 specifically existing in cluster III and motif 1 being excluded from cluster IV. These results indicated the possible functional specification of BnPP2s. A transcriptome data analysis showed that the genes in clusters II to IV exhibited dynamic expression alternation in tissues and the stimulation of S. sclerotiorum, suggesting that they could participate in SD resistance. A GWAS analysis of a rapeseed population comprising 324 accessions identified four BnPP2 genes that were potentially responsible for SD resistance and a transgenic study that was conducted by transiently expressing BnPP2-6 in tobacco (Nicotiana tabacum) leaves validated their positive role in regulating SD resistance in terms of reduced lesion size after inoculation with S. sclerotiorum hyphal plugs. This study provides useful information on PP2 gene functions in B. napus and could aid elaborated functional studies on the PP2 gene family.

Expression Profile of Sorghum Genes and Cis-Regulatory Elements under Salt-Stress Conditions

Salinity stress is one of the most important abiotic stresses that causes great losses in crop production worldwide. Identifying the molecular mechanisms of salt resistance in sorghum will help develop salt-tolerant crops with high yields. Sorghum (Sorghum bicolor (L.) Moench) is one of the world’s four major grains and is known as a plant with excellent adaptability to salt stress. Among the various genotypes of sorghum, a Korean cultivar Nampungchal is also highly tolerant to salt. However, little is known about how Nampungchal responds to salt stress. In this study, we measured various physiological parameters, including Na⁺ and K⁺ contents, in leaves grown under saline conditions and investigated the expression patterns of differentially expressed genes (DEGs) using QuantSeq analysis. These DEG analyses revealed that genes up-regulated in a 150 mM NaCl treatment have various functions related to abiotic stresses, such as ERF and DREB. In addition, transcription factors such as ABA, WRKY, MYB, and bZip bind to the CREs region of sorghum and are involved in the regulation of various abiotic stress-responsive transcriptions, including salt stress. These findings may deepen our understanding of the mechanisms of salt tolerance in sorghum and other crops.

Plant E3 Ligases and Their Role in Abiotic Stress Response

Plants, as sessile organisms, have limited means to cope with environmental changes. Consequently, they have developed complex regulatory systems to ameliorate abiotic stresses im-posed by environmental changes. One such system is the ubiquitin proteasome pathway, which utilizes E3 ligases to target proteins for proteolytic degradation via the 26S proteasome. Plants ex-press a plethora of E3 ligases that are categorized into four major groups depending on their structure. They are involved in many biological and developmental processes in plants, such as DNA repair, photomorphogenesis, phytohormones signaling, and biotic stress. Moreover, many E3 ligase targets are proteins involved in abiotic stress responses, such as salt, drought, heat, and cold. In this review, we will provide a comprehensive overview of E3 ligases and their substrates that have been connected with abiotic stress in order to illustrate the diversity and complexity of how this pathway enables plant survival under stress conditions.

Thymol improves salinity tolerance of tobacco by increasing the sodium ion efflux and enhancing the content of nitric oxide and glutathione

BACKGROUND AND OBJECTIVE

Salt stress is one of the most important abiotic stresses affecting the yield and quality of tobacco (Nicotiana tabacum). Thymol (a natural medicine) has been widely used in medical research because of its antibacterial and anti-inflammatory activities. However, the influence of thymol on the root growth of tobacco is not fully elucidated. In this study, the regulatory effects of different concentrations of thymol were investigated.

METHODOLOGY

Here, histochemical staining and biochemical methods, non-invasive micro-test technology (NMT), and qPCR assay were performed to investigate the effect of thymol and mechanism of it improving salinity tolerance in tobacco seedlings.

RESULTS

In this study, our results showed that thymol rescued root growth from salt stress by ameliorating ROS accumulation, lipid peroxidation, and cell death. Furthermore, thymol enhanced contents of NO and GSH to repress ROS accumulation, further protecting the stability of the cell membrane. And, thymol improved Na+ efflux and the expression of SOS1, HKT1, and NHX1, thus protecting the stability of Na+ and K+.

CONCLUSION

Our study confirmed the protecting effect of thymol in tobacco under salt stress, and we also identified the mechanism of it, involving dynamic regulation of antioxidant system and the maintenance of Na+ homeostasis. It can be a new method to improve salinity tolerance in plants.

Integrated physiological and transcriptomic analyses of two warm- and cool-season turfgrass species in response to heat stress

Warm- and cool-season turfgrasses were originated from different locations with contrasting heat tolerance. The molecular mechanisms of heat tolerance have not been extensively studied in turfgrass species. In this study, transcriptomic analysis showed that bermudagrass was more tolerant to heat stress as evidenced by lower contents of H₂O₂, proline and glutathione than those in tall fescue after heat treatment. RNA sequencing analysis revealed that 32.7% and 17.7% more genes were changed in tall fescue than in bermudagrass after 2 and 12h heat treatment, respectively. GO terms of redox were enriched in bermudagrass whereas metabolite transportation ones were over-represented in tall fescue after 2h treatment. Ubiquitin dependent degradation pathways were commonly regulated in both grass species. CdF-box and FaF-box transgenic Arabidopsis exhibited improved tolerance to heat stress. Regulatory elements analysis revealed that four ABA-responsive elements present in CdF-box promoter, indicating CdF-box could be potentially regulated by ABRE binding factors (ABFs). All these findings provide evidences for understanding heat stress response in warm- and cool-season grass species.

Salt responsive alternative splicing of a RING finger E3 ligase modulates the salt stress tolerance by fine-tuning the balance of COP9 signalosome subunit 5A

Increasing evidence points to the tight relationship between alternative splicing (AS) and the salt stress response in plants. However, the mechanisms linking these two phenomena remain unclear. In this study, we have found that Salt-Responsive Alternatively Spliced gene 1 (SRAS1), encoding a RING-Type E3 ligase, generates two splicing variants: SRAS1.1 and SRAS1.2, which exhibit opposing responses to salt stress. The salt stress-responsive AS event resulted in greater accumulation of SRAS1.1 and a lower level of SRAS1.2. Comprehensive phenotype analysis showed that overexpression of SRAS1.1 made the plants more tolerant to salt stress, whereas overexpression of SRAS1.2 made them more sensitive. In addition, we successfully identified the COP9 signalosome 5A (CSN5A) as the target of SRAS1. CSN5A is an essential player in the regulation of plant development and stress. The full-length SRAS1.1 promoted degradation of CSN5A by the 26S proteasome. By contrast, SRAS1.2 protected CSN5A by competing with SRAS1.1 on the same binding site. Thus, the salt stress-triggered AS controls the ratio of SRAS1.1/SRAS1.2 and switches on and off the degradation of CSN5A to balance the plant development and salt tolerance. Together, these results provide insights that salt-responsive AS acts as post-transcriptional regulation in mediating the function of E3 ligase.

High salinity severely affects plant growth and development, impairing crop production worldwide. E3 ligase is a stress-responsive regulator through ubiquitin-proteasome system for selective protein degradation. The E3s are regulated by transcriptional regulation and post-translational modifications. Here, we have discovered that stress-responsive AS acts as a post-transcriptional regulation modulating the function of E3 ligases. Intriguingly, the truncated proteins generated by salt-responsive AS play opposite roles compared with the full-length E3 ligase. The truncated isoform losing key domain could not degrade the target protein, instead, it interacts and competes with the E3 ligase through binding the same domain of the targets. This finding contributes significantly to a deeper mechanistic understanding of how AS regulates the function of E3 ligase in response to salt stress.

The TCP transcription factor PeTCP10 modulates salt tolerance in transgenic Arabidopsis

PeTCP10 can be induced by salt stresses and play important regulation roles in salt stresses response in transgenic Arabidopsis. Salt stress is one of the major adverse environmental factors that affect normal plant development and growth. PeTCP10, a Class I TCP member, was markedly expressed in moso bamboo mature leaf, root and stem under normal conditions and also induced by salt stress. Overexpressed PeTCP10 was found to enhance salt tolerance of transgenic Arabidopsis at the vegetative growth stage. It was also found capable to increase relative water content, while decreasing relative electrolyte leakage and Na⁺ accumulation of transgenic Arabidopsis versus wild-type (WT) plants at high-salt conditions. In addition, it improved antioxidant capacity of transgenic Arabidopsis plants by promoting catalase activity and enhanced their H₂O₂ tolerance. In contrast to WT plants, transcriptome analysis demonstrated that multiple genes related to abscisic acid, salt and H₂O₂ response were induced after NaCl treatment in transgenic plants. Meanwhile, overexpressed PeTCP10 improved the tolerance of abscisic acid. Moreover, luciferase reporter assay results showed that PeTCP10 is able to directly activate the expression of BT2 in transgenic plants. In contrary, the germination rates of transgenic plants were significantly lower than those of WT plants under high-NaCl conditions. Both primary root length and survival rate at the seedling stage are also found lower in transgenic plants than in WT plants. It is concluded that overexpressed PeTCP10 enhances salt stress tolerance of transgenic plants at the vegetative growth stage, and it also improves salt sensitiveness in both germination and seedling stages. These research results will contribute to further understand the functions of TCPs in abiotic stress response.

Interactions between ShPP2-1, an F-box family gene, and ACR11A regulate cold tolerance of tomato

There is a critical need to identify germplasm resources and genes that promote cold tolerance of tomato because global tomato production is threatened by cold stress. We found that the expression of an F-box gene family member named ShPP2-1 from Solanum habrochaites is cold inducible and studied its contribution to cold tolerance. Overexpression of ShPP2-1 in cultivated tomato (AC) reduced cold tolerance by intensifying damage to cell membranes. To explore the underlying molecular mechanism, we conducted a yeast two-hybrid library screen and found that a protein containing ACT domain repeats named ACR11A interacts with PP2-1. Overexpression of SlACR11A in AC enhanced the cold tolerance of seedlings and germinating seeds. Cold tolerance decreased in tomato plants that overexpressed both of these genes. Additionally, we performed seed germination experiments in the cold with 177 tomato accessions and identified two alleles of SlACR11A that differ in one single-nucleotide polymorphism. We found that one of these alleles, SlACR11A^G, is significantly enriched in cold-tolerant tomato plants. Taken together, our findings indicate that the combination of low expression levels of PP2-1 and high expression levels of ACR11A can promote cold tolerance. These genes may therefore serve as direct targets for both genetic engineering and improvement projects that aim to enhance the cold tolerance of tomato.

Identification, evolutionary profiling, and expression analysis of F-box superfamily genes under phosphate deficiency in tomato

F-box genes are an integral component of the Skp1-cullin-F-box (SCF) complex in eukaryotes. These genes are primarily involved in determining substrate specificities during cellular proteolysis. Here we report that 410 members constitute the F-box superfamily in tomato. Based on the incidence of C-terminal domains, these genes fell into ten subfamilies, leucine-rich repeat domain-containing F-box members constituting the largest subfamily. The F-box genes are present on all 12 chromosomes with varying gene densities. Both segmental and tandem duplication events contribute significantly to their expansion in the tomato genome. The syntenic analysis revealed close relationships among F-box homologs within Solanaceae species genomes. Transcript profiling of F-box members identified several ripening-associated genes with altered expression in the ripening mutants. RNA-sequencing data analysis showed that phosphate (Pi) deficiency affected 55 F-box transcripts in the Pi-deficient seedlings compared to their control seedlings. The persistent up-regulation of eight members, including two phloem protein 2B (PP2-B) genes, PP2-B15, and MATERNAL EFFECT EMBRYO ARREST 66 (MEE66) homologs, at multiple time-points in the roots, shoot, and seedling, point towards their pivotal roles in Pi starvation response in tomato. The attenuation of such upregulation in sucrose absence revealed the necessity of this metabolite for robust activation of these genes in the Pi-deficient seedlings. Altogether, this study identifies novel F-box genes with potential roles in fruit ripening and Pi starvation response and unlocks new avenues for functional characterization of candidate genes in tomato and other related species.

Role of ubiquitination enzymes in abiotic environmental interactions with plants

Ubiquitination, a post-translational modification, plays a crucial role in various aspects of plant development and stress responses. Protein degradation by ubiquitination is well established and ubiquitin is the main underlying component directing the turnover of proteins. Recent reports have also revealed the non-proteolytic roles of ubiquitination in plants. In the past decade, ubiquitination has emerged to be one of the most important players in modulating plant's responses to abiotic stresses, which led to identification of specific E3 ligases and their targets involved in the process. Most of the E3 ligases play regulatory roles by modifying the stability and accumulation of stress responsive regulatory proteins, such as transcription factors, thus, modifying the downstream responses, or by degrading the proteins involved in the downstream cascade itself. In this review, we summarize and highlight the recent advances in the field of ubiquitination-mediated regulation of plant's responses to various abiotic stresses including limited nutrient availability and metal toxicity. The non-proteolytic role of ubiquitination in epigenetic regulation of abiotic stress induced response has also been discussed.

Analysis of N6-methyladenosine reveals a new important mechanism regulating the salt tolerance of sweet sorghum

The N⁶-methyladenosine (m⁶A) modification is the most common internal post-transcriptional modification, with important regulatory effects on RNA export, splicing, stability, and translation. Studies on the m⁶A modifications in plants have focused on Arabidopsis thaliana growth and development. However, A. thaliana is a salt-sensitive and model plant species. Thus, studies aimed at characterizing the role of the m⁶A modification in the salt stress responses of highly salt-tolerant crop species are needed. Sweet sorghum is cultivated as an energy and forage crop, which is highly suitable for growth on saline-alkaline land. Exploring the m⁶A modification in sweet sorghum may be important for elucidating the salt-resistance mechanism of crops. In this study, we mapped the m⁶A modifications in two sorghum genotypes (salt-tolerant M-81E and salt-sensitive Roma) that differ regarding salt tolerance. The m⁶A modification in sweet sorghum under salt stress was drastically altered, especially in Roma, where the m⁶A modification on mRNAs of some salt-resistant related transcripts increased, resulting in enhanced mRNA stability, which in turn was involved in the regulation of salt tolerance in sweet sorghum. Although m⁶A modifications are important for regulating sweet sorghum salt tolerance, the regulatory activity is limited by the initial m⁶A modification level. Additionally, in M-81E and Roma, the differences in the m⁶A modifications were much greater than the differences in gene expression levels and are more sensitive. Our study suggests that the number and extent of m⁶A modifications on the transcripts of salt-resistance genes may be important factors for determining and assessing the salt tolerance of crops.

Genome-wide characterization of the hyperaccumulator Sedum alfredii F-box family under cadmium stress

The F-box genes, which form one of the largest gene families in plants, are vital for plant growth, development and stress response. However, F-box gene family in Sedum alfredii remains unknown. Comprehensive studies addressing their function responding to cadmium stress is still limited. In the present study, 193 members of the F-box gene (SaFbox) family were identified, which were classified into nine subfamilies. Most of the SaFboxs had highly conserved domain and motif. Various functionally related cis-elements involved in plant growth regulation, stress and hormone responses were located in the upstream regions of SaFbox genes. RNA-sequencing and co-expression network analysis revealed that the identified SaFbox genes would be involved in Cd stress. Expression analysis of 16 hub genes confirmed their transcription level in different tissues. Four hub genes (SaFbox40, SaFbox51, SaFbox136 and SaFbox170) were heterologously expressed in a Cd-sensitive yeast cell to assess their effects on Cd tolerance. The transgenic yeast cells carrying SaFbox40, SaFbox51, SaFbox136, or SaFbox170 were more sensitive and accumulated more cadmium under Cd stress than empty vector transformed control cells. Our results performed a comprehensive analysis of Fboxs in S. alfredii and identified their potential roles in Cd stress response.

TaMYB86B encodes a R2R3-type MYB transcription factor and enhances salt tolerance in wheat

The MYB transcription factor family is important for plant responses to abiotic stresses. In this study, we identified three wheat TaMYB86 genes encoding R2R3-type MYB transcription factors. Analyses of the phylogenetic relationships and gene structures of TaMYB86A, TaMYB86B, and TaMYB86D revealed considerable similarities in gene structures and the encoded amino acid sequences. Additionally, TaMYB86B was highly expressed in the roots, stems, and leaves, suggesting it is critical for regulating salt stress responses in wheat. Moreover, TaMYB86B expression was induced by NaCl, abscisic acid (ABA), methyl jasmonate (MeJA), gibberellin (GA), auxin and low temperature treatments. The TaMYB86B protein localized in the nucleus and exhibited transcriptional activation activity. Under salt stress, TaMYB86B-overexpressing plants had a higher biomass and potassium ion (K⁺) content, but lower MDA, H₂O₂, O₂^-., and sodium ion (Na⁺) contents, when compared with the wild-type plants. Quantitative real-time PCR results indicated that the overexpression of TaMYB86B improved the expression of many stress-related genes. These findings suggest that TaMYB86B influences the salt tolerance of wheat by regulating the ion homeostasis to maintain an appropriate osmotic balance and decrease ROS levels.

The F-box protein EST1 modulates salt tolerance in Arabidopsis by regulating plasma membrane Na+/H+ antiport activity

F-box protein, one of the building blocks of the SCF complex, functions in substrate recognition of the SCF subtype of E3 ubiquitin ligase. However, the role of F-box protein in salt stress is largely elusive in plants. Here, we report the characterization of an Arabidopsis salt-tolerant mutant est1 with significantly reduced sodium content and higher Na⁺/H⁺ antiporter activity after NaCl treatment compared to the wild-type. Over-expression of EST1 resulted in increased sensitivity to salt stress, suggesting that EST1 may act as a negative regulator for salt tolerance in Arabidopsis. EST1 encodes an F-box protein, which interacts with ASK4, ASK14, and ASK18, and is likely targeted to the endoplasmic reticulum. In addition, EST1 interacts with MKK4 and negatively regulates MKK4 protein levels and the activity of the plasma membrane Na⁺/H⁺ antiporter. Our findings demonstrate the existence of an EST1-MKK4 module that mediates salt sensitivity by regulating the activity of the plasma membrane Na⁺/H⁺ antiporter. These results provide important information for engineering salt-tolerant crops.

The SUPPRESSOR of MAX2 1 (SMAX1)-Like SMXL6, SMXL7 and SMXL8 Act as Negative Regulators in Response to Drought Stress in Arabidopsis

Drought represents a major threat to crop growth and yields. Strigolactones (SLs) contribute to regulating shoot branching by targeting the SUPPRESSOR OF MORE AXILLARY GROWTH2 (MAX2)-LIKE6 (SMXL6), SMXL7 and SMXL8 for degradation in a MAX2-dependent manner in Arabidopsis. Although SLs are implicated in plant drought response, the functions of the SMXL6, 7 and 8 in the SL-regulated plant response to drought stress have remained unclear. Here, we performed transcriptomic, physiological and biochemical analyses of smxl6, 7, 8 and max2 plants to understand the basis for SMXL6/7/8-regulated drought response. We found that three D53 (DWARF53)-Like SMXL members, SMXL6, 7 and 8, are involved in drought response as the smxl6smxl7smxl8 triple mutants showed markedly enhanced drought tolerance compared to wild type (WT). The smxl6smxl7smxl8 plants exhibited decreased leaf stomatal index, cuticular permeability and water loss, and increased anthocyanin biosynthesis during dehydration. Moreover, smxl6smxl7smxl8 were hypersensitive to ABA-induced stomatal closure and ABA responsiveness during and after germination. In addition, RNA-sequencing analysis of the leaves of the D53-like smxl mutants, SL-response max2 mutant and WT plants under normal and dehydration conditions revealed an SMXL6/7/8-mediated network controlling plant adaptation to drought stress via many stress- and/or ABA-responsive and SL-related genes. These data further provide evidence for crosstalk between ABA- and SL-dependent signaling pathways in regulating plant responses to drought. Our results demonstrate that SMXL6, 7 and 8 are vital components of SL signaling and are negatively involved in drought responses, suggesting that genetic manipulation of SMXL6/7/8-dependent SL signaling may provide novel ways to improve drought resistance.

The wheat E3 ligase TaPUB26 is a negative regulator in response to salt stress in transgenic Brachypodium distachyon

Various abiotic stresses, including high salinity, affect the growth and yield of crop plants. We isolated a gene, TaPUB26, from wheat that encodes a protein containing a U-box domain and armadillo (ARM) repeats. The TaPUB26 transcript levels were upregulated by high salinity, temperature, drought and phytohormones, suggesting the involvement of TaPUB26 in abiotic stress responses. An in vitro ubiquitination assay revealed that TaPUB26 is an E3 ubiquitin ligase. We overexpressed TaPUB26 in Brachypodium distachyon to evaluate TaPUB26 regulation of salt stress tolerance. Compared with the wild type (WT) line, the overexpression lines showed higher salt stress sensitivity under salt stress conditions, but lower chlorophyll (Chl) content, lower photosynthetic levels and overall reduced salt stress tolerance. Additionally, the transgenic plants showed more severe membrane damage, lower antioxidant enzyme activity and more reactive oxygen species (ROS) accumulation than WT plants under salt stress, which might be related to the changes in the expression levels of some antioxidant genes. In addition, the transgenic plants also had higher Na⁺ and lower K⁺ contents, thus maintaining a higher cytosolic Na⁺/K⁺ ratio in leaves and roots than that in WT plants. Further analysis of the molecular mechanisms showed that TaPUB26 interacted with TaRPT2a, an ATPase subunit of the 26S proteasome complex in wheat. We speculated that TaPUB26 negatively regulates salt stress tolerance by interacting with other proteins, such as TaRPT2a, and that this mechanism involves altered antioxidant competition and cytosolic Na⁺/K⁺ equilibrium.

Overexpression of wheat α-mannosidase gene TaMP impairs salt tolerance in transgenic Brachypodium distachyon

The TaMP gene from wheat encodes an α-mannosidase induced by salt stress that functions as negative regulator of salt tolerance in plants. Salt stress significantly affects growth and yield of crop plants. The α-mannosidases function in protein folding, trafficking, and endoplasmic reticulum-associated degradation in eukaryotic cells, and they are involved in abiotic stress tolerance in plants. Previously, we identified the α-mannosidase gene TaMP in wheat (Triticum aestivum). In this study, we investigated the function of TaMP in salt stress tolerance. TaMP expression was induced in wheat leaves by salt, drought, abscisic acid, and H₂O₂ treatments. Overexpressing TaMP in Brachypodium distachyon was associated with a salt-sensitive phenotype. Under salt stress, the overexpressing plants had reduced height, delayed growth status, low photosynthetic rate, decreased survival rate, and diminished yield. Moreover, the overexpression of TaMP aggravated the tendency for ions to become toxic under salt stress by significantly affecting the Na⁺ and K⁺ contents in cells. In addition, TaMP could negatively regulate salt tolerance by affecting the antioxidant enzyme system capacity and increasing the reactive oxygen species accumulation. Our study was helpful to understand the underlying physiological and molecular mechanisms of salt stress tolerance in plants.

The involvement of wheat U-box E3 ubiquitin ligase TaPUB1 in salt stress tolerance

U-box E3 ubiquitin ligases play important roles in the ubiquitin/26S proteasome machinery and in abiotic stress responses. TaPUB1-overexpressing wheat (Triticum aestivum L.) were generated to evaluate its function in salt tolerance. These plants had more salt stress tolerance during seedling and flowering stages, whereas the TaPUB1-RNA interference (RNAi)-mediated knock-down transgenic wheat showed more salt stress sensitivity than the wild type (WT). TaPUB1 overexpression upregulated the expression of genes related to ion channels and increased the net root Na⁺ efflux, but decreased the net K⁺ efflux and H⁺ influx, thereby maintaining a low cytosolic Na⁺ /K⁺ ratio, compared with the WT. However, RNAi-mediated knock-down plants showed the opposite response to salt stress. TaPUB1 could induce the expression of some genes that improved the antioxidant capacity of plants under salt stress. TaPUB1 also interacted with TaMP (Triticum aestivum α-mannosidase protein), a regulator playing an important role in salt response in yeast and in plants. Thus, low cytosolic Na⁺ /K⁺ ratios and better antioxidant enzyme activities could be maintained in wheat with overexpression of TaPUB1 under salt stress. Therefore, we conclude that the U-box E3 ubiquitin ligase TaPUB1 positively regulates salt stress tolerance in wheat.

Salinity tolerance in barley during germination- homologs and potential genes

Salinity affects more than 6% of the world's total land area, causing massive losses in crop yield. Salinity inhibits plant growth and development through osmotic and ionic stresses; however, some plants exhibit adaptations through osmotic regulation, exclusion, and translocation of accumulated Na+ or Cl-. Currently, there are no practical, economically viable methods for managing salinity, so the best practice is to grow crops with improved tolerance. Germination is the stage in a plant's life cycle most adversely affected by salinity. Barley, the fourth most important cereal crop in the world, has outstanding salinity tolerance, relative to other cereal crops. Here, we review the genetics of salinity tolerance in barley during germination by summarizing reported quantitative trait loci (QTLs) and functional genes. The homologs of candidate genes for salinity tolerance in Arabidopsis, soybean, maize, wheat, and rice have been blasted and mapped on the barley reference genome. The genetic diversity of three reported functional gene families for salt tolerance during barley germination, namely dehydration-responsive element-binding (DREB) protein, somatic embryogenesis receptor-like kinase and aquaporin genes, is discussed. While all three gene families show great diversity in most plant species, the DREB gene family is more diverse in barley than in wheat and rice. Further to this review, a convenient method for screening for salinity tolerance at germination is needed, and the mechanisms of action of the genes involved in salt tolerance need to be identified, validated, and transferred to commercial cultivars for field production in saline soil.

Quantitative trait loci for seeding root traits and the relationships between root and agronomic traits in common wheat

A completely developed and vigorous root system can provide a stable platform for aboveground plant organs. To identify loci controlling root traits that could be used in wheat (Triticum aestivum L.) breeding, 199 recombinant inbred lines were used to measure and analyze eight root traits. A total of 18 quantitative trait loci (QTL) located on chromosomes 1A, 2A, 2B, 2D, 4B, 4D, 6A, 7A, and 7B were identified. The phenotypic variation explained by these 18 QTL ranged from 3.27% to 11.75%, and the logarithm of odds scores ranged from 2.50 to 6.58. A comparison of physical intervals indicated several new QTL for root traits were identified. In addition, significant correlations between root and agronomic traits were detected and discussed. The results presented in this study, along with those of previous reports, suggest that chromosomes 2 and 7 likely play important roles in the growth and development of wheat roots.

Expansion and Functional Diversification of SKP1-Like Genes in Wheat (Triticum aestivum L.)

The ubiquitin proteasome 26S system (UPS), involving monomeric and multimeric E3 ligases is one of the most important signaling pathways in many organisms, including plants. The SCF (SKP1/Cullin/F-box) multimeric complex is particularly involved in response to development and stress signaling. The SKP1 protein (S-phase kinase-associated protein 1) is the core subunit of this complex. In this work, we firstly identified 92 and 87 non-redundant Triticum aestivumSKP1-like (TaSKP) genes that were retrieved from the latest release of the wheat genome database (International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0) and the genome annotation of the TGAC v1 respectively. We then investigated the structure, phylogeny, duplication events and expression patterns of the SKP1-like gene family in various tissues and environmental conditions using a wheat expression platform containing public data. TaSKP1-like genes were expressed differentially in response to stress conditions, displaying large genomic variations or short insertions/deletions which suggests functional specialization within TaSKP1-like genes. Finally, interactions between selected wheat FBX (F-box) proteins and putative ancestral TaSKP1-like proteins were tested using the yeast two-hybrid (Y2H) system to examine the molecular interactions. These observations suggested that six Ta-SKP1 genes are likely to be ancestral genes, having similar functions as ASK1 and ASK2 in Arabidopsis, OSK1 and OSK20 in rice and PpSKP1 and PpSKP2 in Physcomitrella patens.

CYSTM3 negatively regulates salt stress tolerance in Arabidopsis

CYSTM3, a small mitochondrial protein, acts as a negative regulator in salt stress response by preventing Na⁺ efflux and disturbing reactive oxygen species (ROS) homeostasis in Arabidopsis. Cysteine-rich transmembrane module (CYSTM) is a not well characterized small peptide family in plants. In this study, we identified a novel mitochondrion-localized CYSTM member CYSTM3 from Arabidopsis, which was ubiquitously expressed in different tissues and dramatically induced by salt stress. Transgenic plants overexpressing CYSTM3 (OE) displayed hypersensitivity to salt stress compared with wild type (WT) plants, whereas a knockout mutant cystm3 was more tolerant to high salinity than WT. Moreover, OE lines accumulated higher contents of Na⁺ and ROS than WT and cystm3 upon exposure to high salinity. Further analysis revealed that CYSTM3 could deter root Na⁺ efflux and inhibit the activities of a range of ROS scavenging enzymes in Arabidopsis. In addition, the transcripts of nuclear salt stress-responsive genes were over-activated in cystm3 than those in WT and OE lines. Taken together, Arabidopsis CYSTM3 acts as a negative regulator in salt stress tolerance.

Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand

BACKGROUND

Salt stress, a major plant environmental stress, is a critical constraint for rice productivity. Dissecting the genetic loci controlling salt tolerance in rice for improving productivity, especially at the flowering stage, remains challenging. Here, we conducted a genome-wide association study (GWAS) of salt tolerance based on exome sequencing of the Thai rice accessions.

RESULTS

Photosynthetic parameters and cell membrane stability under salt stress at the flowering stage; and yield-related traits of 104 Thai rice (Oryza sativa L.) accessions belonging to the indica subspecies were evaluated. The rice accessions were subjected to exome sequencing, resulting in 112,565 single nucleotide polymorphisms (SNPs) called with a minor allele frequency of at least 5%. LD decay analysis of the panel indicates that the average LD for SNPs at 20 kb distance from each other was 0.34 (r2), which decayed to its half value (~ 0.17) at around 80 kb. By GWAS performed using mixed linear model, two hundred loci containing 448 SNPs on exons were identified based on the salt susceptibility index of the net photosynthetic rate at day 6 after salt stress; and the number of panicles, filled grains and unfilled grains per plant. One hundred and forty six genes, which accounted for 73% of the identified loci, co-localized with the previously reported salt quantitative trait loci (QTLs). The top four regions that contained a high number of significant SNPs were found on chromosome 8, 12, 1 and 2. While many are novel, their annotation is consistent with potential involvement in plant salt tolerance and in related agronomic traits. These significant SNPs greatly help narrow down the region within these QTLs where the likely underlying candidate genes can be identified.

CONCLUSIONS

Insight into the contribution of potential genes controlling salt tolerance from this GWAS provides further understanding of salt tolerance mechanisms of rice at the flowering stage, which can help improve yield productivity under salinity via gene cloning and genomic selection.

SENSITIVE TO SALT1, An Endoplasmic Reticulum-Localized Chaperone, Positively Regulates Salt Resistance

Salt stress seriously affects plant growth and development. Through genetic screening, we identified and characterized an Arabidopsis (Arabidopsis thaliana) sensitive to salt1 (ses1) mutant. SES1 was ubiquitously expressed and induced by salt treatment. The salt-sensitive phenotype of ses1 was due neither to the overaccumulation of Na⁺ nor to the suppression of salt tolerance-associated genes. SES1 encoded an uncharacterized endoplasmic reticulum (ER)-localized protein. Coinciding with its subcellular distribution, ses1 exhibited overactivation of unfolded protein response genes and was largely influenced by severe ER stress. Biochemical evidence revealed that SES1 functions as an important molecular chaperone to alleviate salt-induced ER stress. Furthermore, the ER stress sensor basic leucine zipper factor17 transactivated SES1 by binding directly to its promoter region. These results provide insights into salt stress responses and ER homeostasis and shed light on the mechanism by which SES1 modulates salt resistance.

Heterologous expression of Brassica juncea annexin, AnnBj2 confers salt tolerance and ABA insensitivity in transgenic tobacco seedlings

Annexins are multifunctional proteins with roles in plant development and alleviation of stress tolerance. In the present communication, we report on the effect of heterologous expression of Brassica juncea annexin, AnnBj2 in tobacco. Transgenic tobacco plants expressing AnnBj2 exhibited salt-tolerant and abscisic acid (ABA)-insensitive phenotype at the seedling stage. Biochemical analysis showed that AnnBj2 transgenic plants retained higher chlorophyll and proline content, and lower malondialdehyde (MDA) levels compared to the null line under salt stress. They exhibited better water retention capacity compared to the null segregant (NS) line. AnnBj2 overexpression altered the transcript levels of several stress-related marker genes involved in reactive oxygen species (ROS) scavenging and abiotic stress signaling. Taken together, these results suggest a positive role for AnnBj2 in salt stress response upon heterologous expression in tobacco.

Identification and Functional Analysis of a Protein Disulfide Isomerase (AtPDI1) in Arabidopsis thaliana

Protein disulfide isomerase (PDI) catalyzes the conversion of thiol-disulfide and plays an important role in various physiological events in animals. A PDI (OaPDI) from a tropical plant was detailed studied and it was found to be involved in response of biotic stress (Gruber et al., 2007). However, the activities of PDI related to physiological functions in plants are poorly understood. In the present study, a homolog of human PDI in Arabidopsis (AtPDI1), encoded by the gene (At3g54960), was characterized. The recombinant AtPDI1 protein had disulfide isomerase activity in vitro and two pairs of conservative cysteines in catalytic domains play a crucial role in the PDI activities. Expression of AtPDI1 in Escherichia coli significantly enhanced stress tolerance of cells and the mutations of critical cysteines almost lose this function. In plants, AtPDI1 was strongly induced by abiotic stresses and exogenous abscisic acid. An ArabidopsisAtPDI1 knockdown mutant (pdi1) and overexpression lines of transgenic plants obtained by this investigation were used to further examine the function of AtPDI1. The mutant line was more sensitive to stresses than the wild-type, while overexpressing AtPDI1 increased tolerance of seedlings to abiotic stresses, with a higher germination ratio and longer length of roots than the wild-type. Our results suggested AtPDI1 played roles in anti-stresses in Arabidopsis, which relate to the activities of PDI.

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

In plants, various proteins are regulated by the ubiquitin-mediated system in response to different environmental stresses, such as drought, cold and heat. The Skp1-Cullin-F-box (SCF) complex, one of the multisubunit E3 ligases, has been shown to be involved in abiotic response pathways. In this study, Glycine max SKP1-like 1 (GmSK1), which had the typical characteristics of an SKP1 protein, with an alpha/beta structure, targeted to the cytoplasm and nucleus, was isolated from soybean [Glycine max (L.)]. GmSK1 was constitutively expressed in all the tested tissues, especially in the roots. Furthermore, the expression of GmSK1 was simultaneously induced by abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), NaCl, low temperatures and drought, which suggests important roles for GmSK1 in plant responses to hormone treatments and abiotic stress. GmSK1-overexpressing transgenic tobacco (Nicotiana tobacum cv. Samsun) plants showed enhanced tolerance to high salinity and drought stress; exhibited significantly reduced inhibition of growth, greenness and water loss; and exhibited increased MDA accumulation compared with wild-type controls. Our results suggest that GmSK1 might play a role in the crosstalk between ubiquitination and abiotic stress responses in plants.

Signaling through plant lectins: modulation of plant immunity and beyond

Lectins constitute an abundant group of proteins that are present throughout the plant kingdom. Only recently, genome-wide screenings have unraveled the multitude of different lectin sequences within one plant species. It appears that plants employ a plurality of lectins, though relatively few lectins have already been studied and functionally characterized. Therefore, it is very likely that the full potential of lectin genes in plants is underrated. This review summarizes the knowledge of plasma membrane-bound lectins in different biological processes (such as recognition of pathogen-derived molecules and symbiosis) and illustrates the significance of soluble intracellular lectins and how they can contribute to plant signaling. Altogether, the family of plant lectins is highly complex with an enormous diversity in biochemical properties and activities.

Transgene Pyramiding of Salt Responsive Protein 3-1 (SaSRP3-1) and SaVHAc1 From Spartina alterniflora L. Enhances Salt Tolerance in Rice

The transgenic technology using a single gene has been widely used for crop improvement. But the transgenic pyramiding of multiple genes, a promising alternative especially for enhancing complexly inherited abiotic stress tolerance, has received little attention. Here, we developed and evaluated transgenic rice lines with a single Salt Responsive Protein 3-1 (SaSRP3-1) gene as well as pyramids with two-genes SaSRP3-1 and Vacuolar H⁺-ATPase subunit c1 (SaVHAc1) derived from a halophyte grass Spartina alterniflora L. for salt tolerance at seedling, vegetative, and reproductive stages. The overexpression of this novel gene SaSRP3-1 resulted in significantly better growth of E. coli with the recombinant plasmid under 600 mM NaCl stress condition compared with the control. During early seedling and vegetative stages, the single gene and pyramided transgenic rice plants showed enhanced tolerance to salt stress with minimal wilting and drying symptoms, improved shoot and root growth, and significantly higher chlorophyll content, relative water content, and K⁺/Na⁺ ratio than the control plants. The salt stress screening during reproductive stage revealed that the transgenic plants with single gene and pyramids had better grain filling, whereas the pyramided plants showed significantly higher grain yield and higher grain weight compared to control plants. Our study demonstrated transgenic pyramiding as a viable approach to achieve higher level of salt tolerance in crop plants.

Efficient modulation of photosynthetic apparatus confers desiccation tolerance in the resurrection plant Boea hygrometrica

Boea hygrometrica (B. hygrometrica) can tolerate severe desiccation and resume photosynthetic activity rapidly upon water availability. However, little is known about the mechanisms by which B. hygrometrica adapts to dehydration and resumes competence upon rehydration. Here we determine how B. hygrometrica deals with oxidative stress, excessive excitation/electron pressures as well as photosynthetic apparatus modulation during dehydration/rehydration. By measuring ROS generation and scavenging efficiency, we found that B. hygrometrica possesses efficient strategies to maintain cellular redox homeostasis. Transmission electron microscopy (TEM) analysis revealed a remarkable alteration of chloroplast architecture and plastoglobules (PGs) accumulation during dehydration/rehydration. Pulse-amplitude modulated (PAM) chlorophyll fluorescence measurements, P700 redox assay as well as chlorophyll fluorescence emission spectra analysis on leaves of B. hygrometrica during dehydration/rehydration were also performed. Results showed that the photochemical activity of PSII as well as photoprotective energy dissipation in PSII undergo gradual inactivation/activation during dehydration/rehydration in B. hygrometrica; PSI activity is relatively induced upon water deficit, and dehydration leads to physical interaction between PSI and LHCII. Furthermore, blue-native polyacrylamide gel electrophoresis (BN-PAGE) and immunoblot analysis revealed that the protein abundance of light harvesting complexes decrease markedly along with internal water deficit to restrict light absorption and attenuate electron transfer, resulting in limited light excitation and repressed photosynthesis. In contrast, many thylakoid proteins remain at a basal level even after full dehydration. Taken together, our study demonstrated that efficient modulation of cellular redox homeostasis and photosynthetic activity confers desiccation tolerance in B. hygrometrica.

TaPUB1, a Putative E3 Ligase Gene from Wheat, Enhances Salt Stress Tolerance in Transgenic Nicotiana benthamiana

High salinity is one of the most severe environmental stresses and limits the growth and yield of diverse crop plants. We isolated a gene named TaPUB1 from wheat (Triticum aestivum L. cv HF9703) that encodes a novel protein containing a U-box domain, the precursor RNA processing 19p (Prp19) superfamily and WD-40 repeats. Real-time reverse transcription-PCR analysis showed that TaPUB1 transcript accumulation was up-regulated by high salinity, drought and phytohormones, suggesting that it plays a role in the abiotic-related defense response. We overexpressed TaPUB1 in Nicotiana benthamiana to evaluate the function of TaPUB1 in the regulation of the salt stress response. Transgenic N. benthamiana plants (OE) with constitutively overexpressed TaPUB1 under the control of the Cauliflower mosaic virus 35S (CaMV 35S) promoter exhibited a higher germination rate, less growth inhibition, less Chl loss and higher photosynthetic capacity than wild-type (WT) plants under salt stress conditions. These results demonstrated the increased tolerance of OE plants to salt stress compared with the WT. The OE plants had lower osmotic potential (OP), reduced Na+ toxicity and less reactive oxygen species accumulation compared with the WT, which may be related to their higher level of osmolytes, lower Na+/K+ ratio and higher antioxidant enzyme activities under salt stress conditions. Consistent with these results, the up-regulated expression of osmic- and antioxidant-related genes in OE plants indicated a role for TaPUB1 in plant salt tolerance.

E3 Ubiquitin Ligases: Ubiquitous Actors in Plant Development and Abiotic Stress Responses

Understanding the precise regulatory mechanisms of plant development and stress responses at the post-translational level is currently a topic of intensive research. Protein ubiquitination, including the sequential performances of ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin ligase (E3) enzymes, is a refined post-translational modification ubiquitous in all eukaryotes. Plants are an integral part of our ecosystem and, as sessile organisms, the ability to perceive internal and external signals and to adapt well to various environmental challenges is crucial for their survival. Over recent decades, extensive studies have demonstrated that protein ubiquitination plays key roles in multiple plant developmental stages (e.g. seed dormancy and germination, root growth, flowering time control, self-incompatibility and chloroplast development) and several abiotic stress responses (e.g. drought and high salinity), by regulating the abundance, activities or subcellular localizations of a variety of regulatory polypeptides and enzymes. Importantly, diverse E3 ligases are involved in these regulatory pathways by mediating phytohormone and light signaling or other pathways. In this updated review, we mainly summarize recent advances in our understanding of the regulatory roles of protein ubiquitination in plant development and plant-environment interactions, and primarily focus on different types of E3 ligases because they play critical roles in determining substrate specificity.

SCFAtPP2-B11 modulates ABA signaling by facilitating SnRK2.3 degradation in Arabidopsis thaliana

The phytohormone abscisic acid (ABA) is an essential part of the plant response to abiotic stressors such as drought. Upon the perception of ABA, pyrabactin resistance (PYR)/PYR1-like (PYL)/regulatory components of ABA receptor (RCAR) proteins interact with co-receptor protein phosphatase type 2Cs to permit activation Snf1-related protein kinase2 (SnRK2) kinases, which switch on ABA signaling by phosphorylating various target proteins. Thus, SnRK2 kinases are central regulators of ABA signaling. However, the mechanisms that regulate SnRK2 degradation remain elusive. Here, we show that SnRK2.3 is degradated by 26S proteasome system and ABA promotes its degradation. We found that SnRK2.3 interacts with AtPP2-B11 directly. AtPP2-B11 is an F-box protein that is part of a SKP1/Cullin/F-box E3 ubiquitin ligase complex that negatively regulates plant responses to ABA by specifically promoting the degradation of SnRK2.3. AtPP2-B11 was induced by ABA, and the knockdown of AtPP2-B11 expression markedly increased the ABA sensitivity of plants during seed germination and postgerminative development. Overexpression of AtPP2-B11 does not affect ABA sensitivity, but inhibits the ABA hypersensitive phenotypes of SnRK2.3 overexpression lines. These results reveal a novel mechanism through which AtPP2-B11 specifically degrades SnRK2.3 to attenuate ABA signaling and the abiotic stress response in Arabidopsis.

Genome-Wide Screening for Lectin Motifs in Arabidopsis thaliana

For more than three decades, served as a model for plant biology research. At present only a few protein families have been studied in detail in . This study focused on all sequences with lectin motifs in the genome of . Based on amino acid sequence similarity (BLASTp searches), 217 putative lectin genes were retrieved belonging to 9 out of 12 different lectin families. The domain organization and genomic distribution for each lectin family were analyzed. Domain architecture analysis revealed that most of these lectin gene sequences are linked to other domains, often belonging to protein families with catalytic activity. Many protein domains identified are known to play a role in stress signaling and defense, suggesting a major contribution of the putative lectins in development and plant defense. This genome-wide screen for different lectin motifs will help to unravel the functional characteristics of lectins. In addition, phylogenetic trees and WebLogos were created and showed that most lectin sequences that share the same domain architecture evolved together. Furthermore, the amino acids responsible for carbohydrate binding are largely conserved. Our results provide information about the evolutionary relationships and functional divergence of the lectin motifs in .

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsisthaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica). The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST), hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins.