Arabidopsis E3 Ubiquitin Ligases PUB22 and PUB23 Negatively Regulate Drought Tolerance by Targeting ABA Receptor PYL9 for Degradation

ABA-regulated MAPK signaling pathway promotes hormesis in sugar beet under cadmium exposure

Sugar beet (Beta vulgaris L.) shows potential as an energy crop for cadmium (Cd) phytoremediation. To elucidate its in vivo response strategy to Cd exposure, seedlings were treated with 1, 3, and 5 mmol/L CdCl2 (Cd-1, Cd-3, and Cd-5) for 6 h, using 0 mmol/L CdCl2 (Cd-0) as the control. The results showed that Cd-3 promoted a unique "hormesis" effect, leading to superior growth performance, increased levels of chlorophyll, soluble protein, and SOD activity, and reduced MDA content in sugar beet, compared to Cd-1, Cd-5, and even Cd-0. GO and KEGG enrichments and PPI networks of transcriptomic analysis revealed that the differentially expressed genes (DEGs) were primarily involved in lipid metabolism, cellular protein catabolism, and photosynthesis. Notably, the MAPK signaling pathway was significantly enriched only under Cd-3, with the up-regulation of ABA-related core gene BvPYL9 and an increase in ABA content after 6 h of Cd exposure. Furthermore, overexpression of BvPYL9 in Arabidopsis thaliana (OE-1 and OE-2) resulted in enhanced growth (fresh weight, dry weight, and root length), as well as higher ABA and soluble protein contents under different Cd treatments. Cd-induced transcriptional responses of BvPYL9 were also evident in OE-1 and OE-2, especially at 10 µmol/L, indicated by qRT-PCR. These findings suggest that ABA-mediated MAPK signaling pathway is activated in response to Cd toxicity, with BvPYL9 being a key factor in the cascade effects for the Cd-induced hormesis in sugar beet.

Research Progress in the Regulation of the ABA Signaling Pathway by E3 Ubiquitin Ligases in Plants

E3 ubiquitin ligases (UBLs), as enzymes capable of specifically recognizing target proteins in the process of protein ubiquitination, play crucial roles in regulating responses to abiotic stresses such as drought, salt, and temperature. Abscisic acid (ABA), a plant endogenous hormone, is essential to regulating plant growth, development, disease resistance, and defense against abiotic stresses, and acts through a complex ABA signaling pathway. Hormone signaling transduction relies on protein regulation, and E3 ubiquitin ligases play important parts in regulating the ABA pathway. Therefore, this paper reviews the ubiquitin-proteasome-mediated protein degradation pathway, ABA-related signaling pathways, and the regulation of ABA-signaling-pathway-related genes by E3 ubiquitin ligases, aiming to provide references for further exploration of the relevant research on how plant E3 ubiquitin ligases regulate the ABA pathway.

Deciphering the mechanism of E3 ubiquitin ligases in plant responses to abiotic and biotic stresses and perspectives on PROTACs for crop resistance

With global climate change, it is essential to find strategies to make crops more resistant to different stresses and guarantee food security worldwide. E3 ubiquitin ligases are critical regulatory elements that are gaining importance due to their role in selecting proteins for degradation in the ubiquitin-proteasome proteolysis pathway. The role of E3 Ub ligases has been demonstrated in numerous cellular processes in plants responding to biotic and abiotic stresses. E3 Ub ligases are considered a class of proteins that are difficult to control by conventional inhibitors, as they lack a standard active site with pocket, and their biological activity is mainly due to protein-protein interactions with transient conformational changes. Proteolysis-targeted chimeras (PROTACs) are a new class of heterobifunctional molecules that have emerged in recent years as relevant alternatives for incurable human diseases like cancer because they can target recalcitrant proteins for destruction. PROTACs interact with the ubiquitin-proteasome system, principally the E3 Ub ligase in the cell, and facilitate proteasome turnover of the proteins of interest. PROTAC strategies harness the essential functions of E3 Ub ligases for proteasomal degradation of proteins involved in dysfunction. This review examines critical advances in E3 Ub ligase research in plant responses to biotic and abiotic stresses. It highlights how PROTACs can be applied to target proteins involved in plant stress response to mitigate pathogenic agents and environmental adversities.

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.

Comparative transcriptome analysis provides molecular insights into heterosis of waterlogging tolerance in Chrysanthemum indicum

BACKGROUND

Heterosis breeding is one of the most important breeding methods for chrysanthemum. To date, the genetic mechanisms of heterosis for waterlogging tolerance in chrysanthemum are still unclear. This study aims to analyze the expression profiles and potential heterosis-related genes of two hybrid lines and their parents with extreme differences in waterlogging tolerance under control and waterlogging stress conditions by RNA-seq.

RESULTS

A population of 140 F1 progeny derived from Chrysanthemum indicum (Nanchang) (waterlogging-tolerant) and Chrysanthemum indicum (Nanjing) (waterlogging-sensitive) was used to characterize the extent of genetic variation in terms of seven waterlogging tolerance-related traits across two years. Lines 98 and 95, respectively displaying positive and negative overdominance heterosis for the waterlogging tolerance traits together with their parents under control and waterlogging stress conditions, were used for RNA-seq. In consequence, the maximal number of differentially expressed genes (DEGs) occurred in line 98. Gene ontology (GO) enrichment analysis revealed multiple stress-related biological processes for the common up-regulated genes. Line 98 had a significant increase in non-additive genes under waterlogging stress, with transgressive up-regulation and paternal-expression dominant patterns being the major gene expression profiles. Further, GO analysis identified 55 and 95 transgressive up-regulation genes that overlapped with the up-regulated genes shared by two parents in terms of responses to stress and stimulus, respectively. 6,640 genes in total displaying maternal-expression dominance patterns were observed in line 95. In addition, 16 key candidate genes, including SAP12, DOX1, and ERF017 which might be of significant importance for the formation of waterlogging tolerance heterosis in line 98, were highlighted.

CONCLUSION

The current study provides a comprehensive overview of the root transcriptomes among F1 hybrids and their parents under waterlogging stress. These findings lay the foundation for further studies on molecular mechanisms underlying chrysanthemum heterosis on waterlogging tolerance.

Apple E3 ligase MdPUB23 mediates ubiquitin-dependent degradation of MdABI5 to delay ABA-triggered leaf senescence

ABSCISIC ACID-INSENSITIVE5 (ABI5) is a core regulatory factor that mediates the ABA signaling response and leaf senescence. However, the molecular mechanism underlying the synergistic regulation of leaf senescence by ABI5 with interacting partners and the homeostasis of ABI5 in the ABA signaling response remain to be further investigated. In this study, we found that the accelerated effect of MdABI5 on leaf senescence is partly dependent on MdbHLH93, an activator of leaf senescence in apple. MdABI5 directly interacted with MdbHLH93 and improved the transcriptional activation of the senescence-associated gene MdSAG18 by MdbHLH93. MdPUB23, a U-box E3 ubiquitin ligase, physically interacted with MdABI5 and delayed ABA-triggered leaf senescence. Genetic and biochemical analyses suggest that MdPUB23 inhibited MdABI5-promoted leaf premature senescence by targeting MdABI5 for ubiquitin-dependent degradation. In conclusion, our results verify that MdABI5 accelerates leaf senescence through the MdABI5-MdbHLH93-MdSAG18 regulatory module, and MdPUB23 is responsible for the dynamic regulation of ABA-triggered leaf senescence by modulating the homeostasis of MdABI5.

Comparative transcriptome analysis reveals nicotine metabolism is a critical component for enhancing stress response intensity of innate immunity system in tobacco

The pyridine alkaloid nicotine acts as one of best-studied plant resistant traits in tobacco. Previous research has shown that NtERF199 and NtERF189, acting as master regulators within the NIC1 and NIC2 locus, quantitatively contribute to nicotine accumulation levels in N. tabacum. Genome editing-created Nic1(Nterf199) and Nic2 (Nterf189) double mutant provides an ideal platform for precisely dissecting the defensive role of nicotine and the connection between the nicotine biosynthetic pathway with other putative metabolic networks. Taking this advantage, we performed a comparative transcriptomic analysis to reevaluate the potential physiological and metabolic changes in response to nicotine synthesis defect by comparing the nic1nic2 and NIC1NIC2 plants. Our findings revealed that nicotine reduction could systematically diminishes the expression intensities of genes associated with stimulus perception, signal transduction and regulation, as well as secondary metabolic flux. Consequently, this global expression reduction might compromise tobacco adaptions to environmental fitness, herbivore resistances, and plant growth and development. The up-regulation of a novel set of stress-responsive and metabolic pathway genes might signify a newly established metabolic reprogramming to tradeoff the detrimental effect of nicotine loss. These results offer additional compelling evidence regarding nicotine's critical defensive role in nature and highlights the tight link between nicotine biosynthesis and gene expression levels of quantitative resistance-related genes for better environmental adaptation.

Integrative regulatory mechanisms of stomatal movements under changing climate

Global climate change-caused drought stress, high temperatures and other extreme weather profoundly impact plant growth and development, restricting sustainable crop production. To cope with various environmental stimuli, plants can optimize the opening and closing of stomata to balance CO2 uptake for photosynthesis and water loss from leaves. Guard cells perceive and integrate various signals to adjust stomatal pores through turgor pressure regulation. Molecular mechanisms and signaling networks underlying the stomatal movements in response to environmental stresses have been extensively studied and elucidated. This review focuses on the molecular mechanisms of stomatal movements mediated by abscisic acid, light, CO2 , reactive oxygen species, pathogens, temperature, and other phytohormones. We discussed the significance of elucidating the integrative mechanisms that regulate stomatal movements in helping design smart crops with enhanced water use efficiency and resilience in a climate-changing world.

Genome-wide analysis of the U-box E3 ligases gene family in potato (Solanum tuberosum L.) and overexpress StPUB25 enhance drought tolerance in transgenic Arabidopsis

BACKGROUND

Plant U-box (PUB) E3 ubiquitin ligases have vital effects on various biological processes. Therefore, a comprehensive and systematic identification of the members of the U-box gene family in potato will help to understand the evolution and function of U-box E3 ubiquitin ligases in plants.

RESULTS

This work identified altogether 74 PUBs in the potato (StPUBs) and examined their gene structures, chromosomal distributions, and conserved motifs. There were seventy-four StPUB genes on ten chromosomes with diverse densities. As revealed by phylogenetic analysis on PUBs within potato, Arabidopsis, tomato (Solanum lycopersicum), cabbage (Brassica oleracea), rice (Oryza sativa), and corn (Zea mays), were clustered into eight subclasses (C1-C8). According to synteny analysis, there were 40 orthologous StPUB genes to Arabidopsis, 58 to tomato, 28 to cabbage, 7 to rice, and 8 to corn. In addition, RNA-seq data downloaded from PGSC were utilized to reveal StPUBs' abiotic stress responses and tissue-specific expression in the doubled-monoploid potato (DM). Inaddition, we performed RNA-seq on the 'Atlantic' (drought-sensitive cultivar, DS) and the 'Qingshu NO.9' (drought-tolerant cultivar, DT) in early flowering, full-blooming, along with flower-falling stages to detect genes that might be involved in response to drought stress. Finally, quantitative real-time PCR (qPCR) was carried out to analyze three candidate genes for their expression levels within 100 mM NaCl- and 10% PEG 6000 (w/v)-treated potato plantlets for a 24-h period. Furthermore, we analyzed the drought tolerance of StPUB25 transgenic plants and found that overexpression of StPUB25 significantly increased peroxidase (POD) activity, reduced ROS (reactive oxygen species) and MDA (malondialdehyde) accumulation compared with wild-type (WT) plants, and enhancing drought tolerance of the transgenic plants.

CONCLUSION

In this study, three candidate genes related to drought tolerance in potato were excavated, and the function of StPUB25 under drought stress was verified. These results should provide valuable information to understand the potato StPUB gene family and investigate the molecular mechanisms of StPUBs regulating potato drought tolerance.

ATL Protein Family: Novel Regulators in Plant Response to Environmental Stresses

Plants actively develop intricate regulatory mechanisms to counteract the harmful effects of environmental stresses. The ubiquitin-proteasome pathway, a crucial mechanism, employs E3 ligases (E3s) to facilitate the conjugation of ubiquitin to specific target substrates, effectively marking them for proteolytic degradation. E3s play critical roles in many biological processes, including phytohormonal signaling and adaptation to environmental stresses. Arabidopsis Toxicosa en Levadura (ATL) proteins, belonging to a subfamily of RING-H2 E3s, actively modulate diverse physiological processes and plant responses to environmental stresses. Despite studies on the functions of certain ATL family members in rice and Arabidopsis, most ATLs still need more comprehensive study. This review presents an overview of the ubiquitin-proteasome system (UPS), specifically focusing on the pivotal role of E3s and associated enzymes in plant development and environmental adaptation. Our study seeks to unveil the active modulation of plant responses to environmental stresses by E3s and ATLs, emphasizing the significance of ATLs within this intricate process. By emphasizing the importance of studying the roles of E3s and ATLs, our review contributes to developing more resilient plant varieties and promoting sustainable agricultural practices while establishing a research roadmap for the future.

SUPPRESSOR OF MAX2 LIKE 6, 7, and 8 Interact with DDB1 BINDING WD REPEAT DOMAIN HYPERSENSITIVE TO ABA DEFICIENT 1 to Regulate the Drought Tolerance and Target SUCROSE NONFERMENTING 1 RELATED PROTEIN KINASE 2.3 to Abscisic Acid Response in Arabidopsis

SUPPRESSOR OF MAX2-LIKE 6, 7, and 8 (SMXL6,7,8) function as repressors and transcription factors of the strigolactone (SL) signaling pathway, playing an important role in the development and stress tolerance in Arabidopsis thaliana. However, the molecular mechanism by which SMXL6,7,8 negatively regulate drought tolerance and ABA response remains largely unexplored. In the present study, the interacting protein and downstream target genes of SMXL6,7,8 were investigated. Our results showed that the substrate receptor for the CUL4-based E3 ligase DDB1-BINDING WD-REPEAT DOMAIN (DWD) HYPERSENSITIVE TO ABA DEFICIENT 1 (ABA1) (DWA1) physically interacted with SMXL6,7,8. The degradation of SMXL6,7,8 proteins were partially dependent on DWA1. Disruption of SMXL6,7,8 resulted in increased drought tolerance and could restore the drought-sensitive phenotype of the dwa1 mutant. In addition, SMXL6,7,8 could directly bind to the promoter of SUCROSE NONFERMENTING 1 (SNF1)-RELATED PROTEIN KINASE 2.3 (SnRK2.3) to repress its transcription. The mutations in SnRK2.2/2.3 significantly suppressed the hypersensitivity of smxl6/7/8 to ABA-mediated inhibition of seed germination. Conclusively, SMXL6,7,8 interact with DWA1 to negatively regulate drought tolerance and target ABA-response genes. These data provide insights into drought tolerance and ABA response in Arabidopsis via the SMXL6,7,8-mediated SL signaling pathway.

Effects of differentially expressed microRNAs induced by rootstocks and silicon on improving chilling tolerance of cucumber seedlings (Cucumis sativus L.)

BACKGROUND

Rootstocks can improve the chilling tolerance of grafted cucumbers, but their effectiveness varies. Rootstocks with strong de-blooming capacity may result in lower chilling tolerance of grafted cucumbers compared to those with weak de-blooming capacity, while also reducing the silicon absorption. However, it remains unclear whether this reduction in chilling tolerance is due to differences in rootstock genotypes or the reduction in silicon absorption.

RESULTS

The chilling tolerance of cucumber seedlings was improved by using rootstocks and silicon nutrition. Rootstocks had a more significant effect than silicon nutrition, and the weak de-blooming rootstock 'Yunnan figleaf gourd' was superior to the strong de-blooming rootstock 'Huangchenggen No. 2'. Compared to self-rooted cucumber, twelve miRNAs were regulated by two rootstocks, including seven identical miRNAs (novel-mir23, novel-mir26, novel-mir30, novel-mir37, novel-mir46, miR395a and miR398a-3p) and five different miRNAs (novel-mir32, novel-mir38, novel-mir65, novel-mir78 and miR397a). Notably, four of these miRNAs (novel-mir38, novel-mir65, novel-mir78 and miR397a) were only identified in 'Yunnan figleaf gourd'-grafted cucumbers. Furthermore, six miRNAs (miR168a-5p, miR390a-5p, novel-mir26, novel-mir55, novel-mir67 and novel-mir70) were found to be responsive to exogenous silicon. Target gene prediction for 20 miRNAs resulted in 520 genes. Functional analysis of these target genes showed that 'Yunnan figleaf gourd' improves the chilling tolerance of cucumber by regulating laccase synthesis and sulfate metabolism, while 'Huangchenggen No. 2' and exogenous silicon reduced chilling stress damage to cucumber by regulating ROS scavenging and protein protection, respectively.

CONCLUSION

Among the identified miRNAs, novel-mir46 and miR398a-3p were found in cucumbers in response to chilling stress and two types of rootstocks. However, no identical miRNAs were identified in response to chilling stress and silicon. In addition, the differential expression of novel-mir38, novel-mir65, novel-mir78 and miR397a may be one of the important reasons for the differences in chilling tolerance of grafted cucumbers caused by two types of rootstocks.

The safflower MBW complex regulates HYSA accumulation through degradation by the E3 ligase CtBB1

The regulatory mechanism of the MBW (MYB-bHLH-WD40) complex in safflower (Carthamus tinctorius) remains unclear. In the present study, we show that the separate overexpression of the genes CtbHLH41, CtMYB63, and CtWD40-6 in Arabidopsis thaliana increased anthocyanin and procyanidin contents in the transgenic plants and partially rescued the trichome reduction phenotype of the corresponding bhlh41, myb63, and wd40-6 single mutants. Overexpression of CtbHLH41, CtMYB63, or CtWD40-6 in safflower significantly increased the content of the natural pigment hydroxysafflor yellow A (HYSA) and negatively regulated safflower petal size. Yeast-two-hybrid, functional, and genetic assays demonstrated that the safflower E3 ligase CtBB1 (BIG BROTHER 1) can ubiquitinate CtbHLH41, marking it for degradation through the 26S proteasome and negatively regulating flavonoid accumulation. CtMYB63/CtWD40-6 enhanced the transcriptional activity of CtbHLH41 on the CtDFR (dihydroflavonol 4-reductase) promoter. We propose that the MBW-CtBB1 regulatory module may play an important role in coordinating HYSA accumulation with other response mechanisms.

BPL3 binds the long non-coding RNA nalncFL7 to suppress FORKED-LIKE7 and modulate HAI1-mediated MPK3/6 dephosphorylation in plant immunity

RNA-binding proteins (RBPs) participate in a diverse set of biological processes in plants, but their functions and underlying mechanisms in plant-pathogen interactions are largely unknown. We previously showed that Arabidopsis thaliana BPA1-LIKE PROTEIN3 (BPL3) belongs to a conserved plant RBP family and negatively regulates reactive oxygen species (ROS) accumulation and cell death under biotic stress. In this study, we demonstrate that BPL3 suppresses FORKED-LIKE7 (FL7) transcript accumulation and raises levels of the cis-natural antisense long non-coding RNA (lncRNA) of FL7 (nalncFL7). FL7 positively regulated plant immunity to Phytophthora capsici while nalncFL7 negatively regulated resistance. We also showed that BPL3 directly binds to and stabilizes nalncFL7. Moreover, nalncFL7 suppressed accumulation of FL7 transcripts. Furthermore, FL7 interacted with HIGHLY ABA-INDUCED PP2C1 (HAI1), a type 2C protein phosphatase, and inhibited HAI1 phosphatase activity. By suppressing HAI1 activity, FL7 increased the phosphorylation levels of MITOGEN-ACTIVATED PROTEIN KINASE 3 (MPK3) and MPK6, thus enhancing immunity responses. BPL3 and FL7 are conserved in all plant species tested, but the BPL3-nalncFL7-FL7 cascade was specific to the Brassicaceae. Thus, we identified a conserved BPL3-nalncFL7-FL7 cascade that coordinates plant immunity.

Calcium decoders and their targets: The holy alliance that regulate cellular responses in stress signaling

Calcium (Ca²⁺) signaling is versatile communication network in the cell. Stimuli perceived by cells are transposed through Ca²⁺-signature, and are decoded by plethora of Ca²⁺ sensors present in the cell. Calmodulin, calmodulin-like proteins, Ca²⁺-dependent protein kinases and calcineurin B-like proteins are major classes of proteins that decode the Ca²⁺ signature and serve in the propagation of signals to different parts of cells by targeting downstream proteins. These decoders and their targets work together to elicit responses against diverse stress stimuli. Over a period of time, significant attempts have been made to characterize as well as summarize elements of this signaling machinery. We begin with a structural overview and amalgamate the newly identified Ca²⁺ sensor protein in plants. Their ability to bind Ca²⁺, undergo conformational changes, and how it facilitates binding to a wide variety of targets is further embedded. Subsequently, we summarize the recent progress made on the functional characterization of Ca²⁺ sensing machinery and in particular their target proteins in stress signaling. We have focused on the physiological role of Ca²⁺, the Ca²⁺ sensing machinery, and the mode of regulation on their target proteins during plant stress adaptation. Additionally, we also discuss the role of these decoders and their mode of regulation on the target proteins during abiotic, hormone signaling and biotic stress responses in plants. Finally, here, we have enumerated the limitations and challenges in the Ca²⁺ signaling. This article will greatly enable in understanding the current picture of plant response and adaptation during diverse stimuli through the lens of Ca²⁺ signaling.

The activity of the stress modulated Arabidopsis ubiquitin ligases PUB46 and PUB48 is partially redundant

The Arabidopsis ubiquitin ligases PUB46, PUB47 and PUB48 are encoded by paralogus genes. Single gene pub46 and pub48 mutants display increased drought sensitivity compared to wild type (WT) suggesting that each has specific biological activity. The high sequence homology between PUB46 and PUB48 activity suggested that they may also share some aspects of their activity. Unfortunately, the close proximity of the PUB46 and PUB48 gene loci precludes obtaining a double mutant required to study if they are partially redundant by crossing the available single mutants. We thus applied microRNA technology to reduce the activity of all three gene products of the PUB46-48 subfamily by constructing an artificial microRNA (aMIR) targeted to this subfamily. Expressing aMIR46-48 in WT plants resulted in increased drought-sensitivity, a phenotype resembling that of each of the single pub46 and pub48 mutants, and enhanced sensitivity to methyl viologen, similar to that observed for the pub46 mutant. The WT plants expressing aMIR46-48 plants also revealed reduced inhibition by ABA at seed germination, a phenotype not evident in the single mutants. Expressing aMIR46-48 in pub46 and pub48 mutants further enhanced the drought sensitivity of each parental single mutant and of WT expressing aMIR46-48. These results suggest that the biological activities of PUB46 and PUB48 in abiotic stress response are partially redundant.

Comparative physiological and coexpression network analyses reveal the potential drought tolerance mechanism of peanut

BACKGROUND

Drought stress has negative effects on plant growth and productivity. In this study, a comprehensive analysis of physiological responses and gene expression was performed. The responses and expressions were compared between drought-tolerant (DT) and drought-sensitive (DS) peanut varieties to investigate the regulatory mechanisms and hub genes involved in the impact of drought stress on culture.

RESULTS

The drought-tolerant variety had robust antioxidative capacities with higher total antioxidant capacity and flavonoid contents, and it enhanced osmotic adjustment substance accumulation to adapt to drought conditions. KEGG analysis of differentially expressed genes demonstrated that photosynthesis was strongly affected by drought stress, especially in the drought-sensitive variety, which was consistent with the more severe suppression of photosynthesis. The hub genes in the key modules related to the drought response, including genes encoding protein kinase, E3 ubiquitin-protein ligase, potassium transporter, pentatricopeptide repeat-containing protein, and aspartic proteinase, were identified through a comprehensive combined analysis of genes and physiological traits using weighted gene co-expression network analysis. There were notably differentially expressed genes between the two varieties, suggesting the positive roles of these genes in peanut drought tolerance.

CONCLUSION

A comprehensive analysis of physiological traits and relevant genes was conducted on peanuts with different drought tolerances. The findings revealed diverse drought-response mechanisms and identified candidate genes for further research.

Identification of Quantitative Trait Locus and Candidate Genes for Drought Tolerance in a Soybean Recombinant Inbred Line Population

With global warming and regional decreases in precipitation, drought has become a problem worldwide. As the number of arid regions in the world is increasing, drought has become a major factor leading to significant crop yield reductions and food crises. Soybean is a crop that is relatively sensitive to drought. It is also a crop that requires more water during growth and development. The aim of this study was to identify the quantitative trait locus (QTL) that affects drought tolerance in soybean by using a recombinant inbred line (RIL) population from a cross between the drought-tolerant cultivar 'Jindou21' and the drought-sensitive cultivar 'Zhongdou33'. Nine agronomic and physiological traits were identified under drought and well-watered conditions. Genetic maps were constructed with 923,420 polymorphic single nucleotide polymorphism (SNP) markers distributed on 20 chromosomes at an average genetic distance of 0.57 centimorgan (cM) between markers. A total of five QTLs with a logarithm of odds (LOD) value of 4.035-8.681 were identified on five chromosomes. Under well-watered conditions and drought-stress conditions, one QTL related to the main stem node number was located on chromosome 16, accounting for 17.177% of the phenotypic variation. Nine candidate genes for drought resistance were screened from this QTL, namely Glyma.16G036700, Glyma.16G036400, Glyma.16G036600, Glyma.16G036800, Glyma.13G312700, Glyma.13G312800, Glyma.16G042900, Glyma.16G043200, and Glyma.15G100700. These genes were annotated as NAC transport factor, GATA transport factor, and BTB/POZ-MATH proteins. This result can be used for molecular marker-assisted selection and provide a reference for breeding for drought tolerance in soybean.

Apple U-box-type E3 ubiquitin ligase MdPUB23 reduces cold-stress tolerance by degrading the cold-stress regulatory protein MdICE1

Cold stress limits plant growth, geographical distribution, and crop yield. The MYC-type bHLH transcription factor ICE1 is recognized as the core positive regulator of the cold-stress response. However, how ICE1 protein levels are regulated remains to be further studied. In this study, we observed that a U-box-type E3 ubiquitin ligase, MdPUB23, positively regulated the cold-stress response in apple. The expression of MdPUB23 increased at both the transcriptional and post-translational levels in response to cold stress. Overexpression of MdPUB23 in transgenic apple enhanced sensitivity to cold stress. Further study showed that MdPUB23 directly interacted with MdICE1, promoting the ubiquitination-mediated degradation of the MdICE1 protein through the 26S-proteasome pathway and reducing the MdICE1-improved cold-stress tolerance in apple. Our results reveal that MdPUB23 regulates the cold-stress response by directly mediating the stability of the positive regulator MdICE1. The PUB23-ICE1 ubiquitination module may play a role in maintaining ICE1 protein homeostasis and preventing overreactions from causing damage to plants. The discovery of the ubiquitination regulatory pathway of ICE1 provides insights for the further exploration of plant cold-stress-response mechanisms.

The E3 Ligase GmPUB21 Negatively Regulates Drought and Salinity Stress Response in Soybean

E3-ubiquitin ligases are known to confer abiotic stress responses in plants. In the present study, GmPUB21, a novel U-box E3-ubiquitin ligase-encoding gene, was isolated from soybean and functionally characterized. The expression of GmPUB21, which possesses E3-ubiquitin ligase activity, was found to be significantly up-regulated by drought, salinity, and ABA treatments. The fusion protein GmPUB21-GFP was localized in the cytoplasm, nucleus, and plasma membrane. Transgenic lines of the Nicotiana benthamiana over-expressing GmPUB21 showed more sensitive to osmotic, salinity stress and ABA in seed germination and inhibited mannitol/NaCl-mediated stomatal closure. Moreover, higher reactive oxygen species accumulation was observed in GmPUB21 overexpressing plants after drought and salinity treatment than in wild-type (WT) plants. Contrarily, silencing of GmPUB21 in soybean plants significantly enhanced the tolerance to drought and salinity stresses. Collectively, our results revealed that GmPUB21 negatively regulates the drought and salinity tolerance by increasing the stomatal density and aperture via the ABA signaling pathway. These findings improved our understanding of the role of GmPUB21 under drought and salinity stresses in soybean.

De novo transcriptome analysis identifies key genes involved in dehydration stress response in kodo millet (Paspalum scrobiculatum L.)

Kodo millet (Paspalum scrobiculatum L.) is a small millet species known for its excellent nutritional and climate-resilient traits. To understand the genes and pathways underlying dehydration stress tolerance of kodo millet, the transcriptome of cultivar 'CO3' subjected to dehydration stress (0 h, 3 h, and 6 h) was sequenced. The study generated 239.1 million clean reads that identified 9201, 9814, and 2346 differentially expressed genes (DEGs) in 0 h vs. 3 h, 0 h vs. 6 h, and 3 h vs. 6 h libraries, respectively. The DEGs were found to be associated with vital molecular pathways, including hormone metabolism and signaling, antioxidant scavenging, photosynthesis, and cellular metabolism, and were validated using qRT-PCR. Also, a higher abundance of uncharacterized genes expressed during stress warrants further studies to characterize this class of genes to understand their role in dehydration stress response. Altogether, the study provides insights into the transcriptomic response of kodo millet during dehydration stress.

PYR/PYL/RCAR Receptors Play a Vital Role in the Abscisic-Acid-Dependent Responses of Plants to External or Internal Stimuli

Abscisic acid (ABA) is a phytohormone that plays a key role in regulating several developmental processes as well as in response to stressful conditions such as drought. Activation of the ABA signaling cascade allows the induction of an appropriate physiological response. The basic components of the ABA signaling pathway have been recognized and characterized in recent years. Pyrabactin resistance, pyrabactin resistance-like, and the regulatory component of ABA receptors (PYR/PYL/RCAR) are the major components responsible for the regulation of the ABA signaling pathway. Here, we review recent findings concerning the PYR/PYL/RCAR receptor structure, function, and interaction with other components of the ABA signaling pathway as well as the termination mechanism of ABA signals in plant cells. Since ABA is one of the basic elements related to abiotic stress, which is increasingly common in the era of climate changes, understanding the perception and transduction of the signal related to this phytohormone is of paramount importance in further increasing crop tolerance to various stress factors.

Expression profiling of TaARGOS homoeologous drought responsive genes in bread wheat

Drought tolerant germplasm is needed to increase crop production, since water scarcity is a critical bottleneck in crop productivity worldwide. Auxin Regulated Gene involved in Organ Size (ARGOS) is a large protein family of transcription factors that plays a vital role in organ size, plant growth, development, and abiotic stress responses in plants. Although, the ARGOS gene family has been discovered and functionalized in a variety of crop plants, but a comprehensive and systematic investigation of ARGOS genes in locally used commercial wheat cultivars is still yet to be reported. The relative expression of three highly conserved TaARGOS homoeologous genes (TaARGOS-A, TaARGOS-B, TaARGOS-D) was studied in three drought-tolerant (Pakistan-2013, NARC-2009 and NR-499) and three sensitive (Borlaug-2016, NR-514 and NR-516) wheat genotypes under osmotic stress, induced by PEG-6000 at 0 (exogenous control), 2, 4, 6, and 12 h. The normalization of target genes was done using β-actin as endogenous control, whereas DREB3, as a marker gene was also transcribed, reinforcing the prevalence of dehydration in all stress treatments. Real-time quantitative PCR revealed that osmotic stress induced expression of the three TaARGOS transcripts in different wheat seedlings at distinct timepoints. Overall, all genes exhibited significantly higher expression in the drought-tolerant genotypes as compared to the sensitive ones. For instance, the expression profile of TaARGOS-A and TaARGOS-D showed more than threefold increase at 2 h and six to sevenfold increase after 4 h of osmotic stress. However, after 6 h of osmotic stress these genes started to downregulate, and the lowest gene expression was noticed after 12 h of osmotic stress. Among all the homoeologous genes, TaARGOS-D, in particular, had a more significant influence on controlling plant growth and drought tolerance as it showed the highest expression. Altogether, TaARGOSs are involved in seedling establishment and overall plant growth. In addition, the tolerant group of genotypes had a much greater relative fold expression than the sensitive genotypes. Ultimately, Pakistan-2013 showed the highest relative expression of the studied genes than other genotypes which shows its proficiency to mitigate osmotic stress. Therefore, it could be cultivated in arid and semi-arid regions under moisture-deficient regimes. These findings advocated the molecular mechanism and regulatory roles of TaARGOS genes in plant growth and osmotic stress tolerance in contrasting groups of wheat genotypes, accompanied by the genetic nature of identified genotypes in terms of their potential for drought tolerance.

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.

Exogenous Melatonin Improves Cold Tolerance of Strawberry (Fragaria × ananassa Duch.) through Modulation of DREB/CBF-COR Pathway and Antioxidant Defense System

The strawberry (Fragaria × ananassa Duch.) is an important fruit crop cultivated worldwide for its unique taste and nutritional properties. One of the major risks associated with strawberry production is cold damage. Recently, melatonin has emerged as a multifunctional signaling molecule that influences plant growth and development and reduces adverse consequences of cold stress. The present study was conducted to investigate the defensive role of melatonin and its potential interrelation with abscisic acid (ABA) in strawberry plants under cold stress. The results demonstrate that melatonin application conferred improved cold tolerance on strawberry seedlings by reducing malondialdehyde and hydrogen peroxide contents under cold stress. Conversely, pretreatment of strawberry plants with 100 μM melatonin increased soluble sugar contents and different antioxidant enzyme activities (ascorbate peroxidase, catalase, and peroxidase) and non-enzymatic antioxidant (ascorbate and glutathione) activities under cold stress. Furthermore, exogenous melatonin treatment stimulated the expression of the DREB/CBF—COR pathways’ downstream genes. Interestingly, ABA treatment did not change the expression of the DREB/CBF—COR pathway. These findings imply that the DREB/CBF-COR pathway confers cold tolerance on strawberry seedlings through exogenous melatonin application. Taken together, our results reveal that melatonin (100 μM) pretreatment protects strawberry plants from the damages induced by cold stress through enhanced antioxidant defense potential and modulating the DREB/CBF—COR pathway.

Aldehyde dehydrogenase 3I1 gene is recruited in conferring multiple abiotic stress tolerance in plants

Plant growth and productivity is restricted by a multitude of abiotic stresses. These stresses negatively affect physiological and metabolic pathways, leading to the production of many harmful substances like ROS, lipid peroxides and aldehydes. This study was conducted to investigate the role of Arabidopsis ALDH3I1 gene in multiple abiotic stress tolerance. Transgenic tobacco plants were generated that overexpress the ALDH3I1 gene driven by the CaMV35S promoter and evaluated under different abiotic stresses, namely salt, drought, cold and oxidative stress. Tolerance to stress was evaluated based on responses of various growth and physiological traits under stress condition. Transgenic plants displayed elevated ALDH3I1 transcript levels compared to WT plants. The constitutive ectopic expression of ALDH3I1 conferred increased tolerance to salt, drought, cold and oxidative stresses in transgenic plants, along with improved plant growth. Transgenic plants overexpressing ALDH3I1 had higher chlorophyll content, photosynthesis rate and proline, and less accumulation of ROS and malondialdehyde compared to the WT, which contributed to stress tolerance in transgenic plants. Our results further revealed that ALDH3I1 had a positive effect on CO₂ assimilation rate in plants under abiotic stress conditions. Overall, this study revealed that ALDH3I1 positively regulates abiotic stress tolerance in plants, and has future implications in producing transgenic cereal and horticultural plants tolerant to abiotic stresses.

Identification and expression analysis of PUB genes in tea plant exposed to anthracnose pathogen and drought stresses

The plant U-box (PUB) gene family, one of the major ubiquitin ligase families in plants, plays important roles in multiple cellular processes including environmental stress responses and resistance. The function of U-box genes has been well characterized in Arabidopsis and other plants. However, little is known about the tea plant (Camellia sinensis) PUB genes. Here, 89 U-box proteins were identified from the chromosome-scale referenced genome of tea plant. According to the domain organization and phylogenetic analysis, the tea plant PUB family were classified into ten classes, named Class I to X, respectively. Using previously released stress-related RNA-seq data in tea plant, we identified 34 stress-inducible CsPUB genes. Specifically, eight CsPUB genes were expressed differentially under both anthracnose pathogen and drought stresses. Moreover, six of the eight CsPUBs were upregulated in response to these two stresses. Expression profiling performed by qRT-PCR was consistent with the RNA-seq analysis, and stress-related cis-acting elements were identified in the promoter regions of the six upregulated CsPUB genes. These results strongly implied the putative functions of U-box ligase genes in response to biotic and abiotic stresses in tea plant.

Comparative transcriptome analysis identified important genes and regulatory pathways for flower color variation in Paphiopedilum hirsutissimum

BACKGROUND

Paphiopedilum hirsutissimum is a member of Orchidaceae family that is famous for its ornamental value around the globe, it is vulnerable due to over-exploitation and was listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents its trade across borders. Variation in flower color that gives rise to different flower patterns is a major trait contributing to its high ornamental value. However, the molecular mechanism underlying color formation in P. hirsutissimum still remains unexplored. In the present study, we exploited natural variation in petal and labellum color of Paphiopedilum plants and used comparative transcriptome analysis as well as pigment measurements to explore the important genes, metabolites and regulatory pathways linked to flower color variation in P. hirsutissimum.

RESULT

We observed that reduced anthocyanin and flavonoid contents along with slightly higher carotenoids are responsible for albino flower phenotype. Comparative transcriptome analysis identified 3287 differentially expressed genes (DEGs) among normal and albino labellum, and 3634 DEGs between normal and albino petals. Two genes encoding for flavanone 3-hydroxylase (F3H) and one gene encoding for chalcone synthase (CHS) were strongly downregulated in albino labellum and petals compared to normal flowers. As both F3H and CHS catalyze essentially important steps in anthocyanin biosynthesis pathway, downregulation of these genes is probably leading to albino flower phenotype via down-accumulation of anthocyanins. However, we observed the downregulation of major carotenoid biosynthesis genes including VDE, NCED and ABA2 which was inconsistent with the increased carotenoid accumulation in albino flowers, suggesting that carotenoid accumulation was probably controlled at post-transcriptional or translational level. In addition, we identified several key transcription factors (MYB73, MYB61, bHLH14, bHLH106, MADS-SOC1, AP2/ERF1, ERF26 and ERF87) that may regulate structural genes involved in flower color formation in P. hirsutissimum. Importantly, over-expression of some of these candidate TFs increased anthocyanin accumulation in tobacco leaves which provided important evidence for the role of these TFs in flower color formation probably via regulating key structural genes of the anthocyanin pathway.

CONCLUSION

The genes identified here could be potential targets for breeding P. hirsutissimum with different flower color patterns by manipulating the anthocyanin and carotenoid biosynthesis pathways.

Phosphoproteomic analysis of ozone stress-responsive mechanisms in grapevine identifies KEG required for stress regulation

The environmental damage caused by ozone is of increasing concern globally. The phosphoproteomics approach was used to explore the mechanisms underlying grapevine tolerance to ozone stress and identify phosphoproteins altered by ozone treatment. Results revealed that 194 of 2275 quantitatively analyzed phosphoproteins were significantly regulated after ozone treatment. Biological pathways related to transport were significantly enriched by the differentially regulated phosphoproteins. Among these phosphoproteins, the phosphorylation of RING E3 ligase in grape (V. vinifera KEEP ON GOING, VvKEG) decreased after ozone treatment. Over-expression of VvKEG in Arabidopsis decreased abscisic acid (ABA) sensitivity and enhanced ozone tolerance. Furthermore, VvKEG interacted with the ABA-responsive transcription factor ABSCISIC ACID-INSENSITIVE3 (ABI3). The exogenous application of ABA on grapevine leaves significantly influenced chlorophyll fluorescence, chlorophyll, and malondialdehyde (MDA) contents under ozone treatment; however, treatment with 150 μmol ABA aggravated ozone stress. These results indicate that phosphorylation modification provides information on ozone-induced processes and that VvKEG plays a critical role in these processes via regulation of the ABA signaling pathway in grape.

Genome-Wide Analysis of the IQM Gene Family in Rice (Oryza sativa L.)

Members of the IQM (IQ-Motif Containing) gene family are involved in plant growth and developmental processes, biotic and abiotic stress response. To systematically analyze the IQM gene family and their expression profiles under diverse biotic and abiotic stresses, we identified 8 IQM genes in the rice genome. In the current study, the whole genome identification and characterization of OsIQMs, including the gene and protein structure, genome localization, phylogenetic relationship, gene expression and yeast two-hybrid were performed. Eight IQM genes were classified into three subfamilies (I-III) according to the phylogenetic analysis. Gene structure and protein motif analyses showed that these IQM genes are relatively conserved within each subfamily of rice. The 8 OsIQM genes are distributed on seven out of the twelve chromosomes, with three IQM gene pairs involved in segmental duplication events. The evolutionary patterns analysis revealed that the IQM genes underwent a large-scale event within the last 20 to 9 million years. In addition, quantitative real-time PCR analysis of eight OsIQMs genes displayed different expression patterns at different developmental stages and in different tissues as well as showed that most IQM genes were responsive to PEG, NaCl, jasmonic acid (JA), abscisic acid (ABA) treatment, suggesting their crucial roles in biotic, and abiotic stress response. Additionally, a yeast two-hybrid assay showed that OsIQMs can interact with OsCaMs, and the IQ motif of OsIQMs is required for OsIQMs to combine with OsCaMs. Our results will be valuable to further characterize the important biological functions of rice IQM genes.

Characterization of Arabidopsis thaliana R2R3 S23 MYB Transcription Factors as Novel Targets of the Ubiquitin Proteasome-Pathway and Regulators of Salt Stress and Abscisic Acid Response

Rapid response to environmental changes and abiotic stress to coordinate developmental programs is critical for plants. To accomplish this, plants use the ubiquitin proteasome pathway as a flexible and efficient mechanism to control protein stability and to direct cellular reactions. Here, we show that all three members of the R2R3 S23 MYB transcription factor subfamily, MYB1, MYB25, and MYB109, are degraded by the 26S proteasome, likely facilitated by a CUL3-based E3 ligase that uses MATH-BTB/POZ proteins as substrate adaptors. A detailed description of MYB1, MYB25, and MYB109 expression shows their nuclear localization and specific tissue specific expression patterns. It further demonstrates that elevated expression of MYB25 reduces sensitivities toward abscisic acid, osmotic and salt stress in Arabidopsis, while downregulation of all S23 members results in hypersensitivities. Transcriptional profiling in root and shoot of seedlings overexpressing MYB25 shows that the transcription factor widely affects cellular stress pathways related to biotic and abiotic stress control. Overall, the work extends our knowledge on proteins targeted by CUL3-based E3 ligases that use MATH-BTB/POZ proteins as substrate adaptors and provides first information on all members of the MYB S23 subfamily.

Wheat TaPUB1 protein mediates ABA response and seed development through ubiquitination

Abscisic acid (ABA) is an important regulator of plant growth, development, and biotic and abiotic stress responses. Ubiquitination plays important roles in regulating ABA signaling. E3 ligase, a key member in ubiquitination, actively participates in the regulation of biosynthesis, de-repression, and activation of ABA response and degradation of signaling components. In this study, we found that that overexpression of wheat E3 ligase TaPUB1 decreased the sensitivity of wheat seedlings to ABA, whereas TaPUB1-RNA interference (TaPUB1-RNAi) lines increased wheat sensitivity to ABA during germination, root growth, and stomatal opening. TaPUB1 influenced the expression of several ABA-responsive genes, and also interacted with TaPYL4 and TaABI5, which are involved in ABA signal transduction, and promoted their degradation. Additionally, we observed that TaPUB1-OE lines resulted in lower single-split grain numbers, larger seed size, and higher thousand kernel weight, when compared with the WT lines. Contrasting results were obtained for TaPUB1-RNAi lines. It suggests that TaPUB1 acts as a negative regulator in the ABA signaling pathway by interacting with TaPYL4 and TaABI5, subsequently affecting seed development in wheat. In addition, the enhanced abiotic tolerance of overexpression lines due to enhanced photosynthesis and root development may be related to the degradation of TaABI5 by TaPUB1.

Growth Promotion or Osmotic Stress Response: How SNF1-Related Protein Kinase 2 (SnRK2) Kinases Are Activated and Manage Intracellular Signaling in Plants

Reversible phosphorylation is a major mechanism for regulating protein function and controls a wide range of cellular functions including responses to external stimuli. The plant-specific SNF1-related protein kinase 2s (SnRK2s) function as central regulators of plant growth and development, as well as tolerance to multiple abiotic stresses. Although the activity of SnRK2s is tightly regulated in a phytohormone abscisic acid (ABA)-dependent manner, recent investigations have revealed that SnRK2s can be activated by group B Raf-like protein kinases independently of ABA. Furthermore, evidence is accumulating that SnRK2s modulate plant growth through regulation of target of rapamycin (TOR) signaling. Here, we summarize recent advances in knowledge of how SnRK2s mediate plant growth and osmotic stress signaling and discuss future challenges in this research field.

Ubiquitylation of ABA Receptors and Protein Phosphatase 2C Coreceptors to Modulate ABA Signaling and Stress Response

Post-translational modifications play a fundamental role in regulating protein function and stability. In particular, protein ubiquitylation is a multifaceted modification involved in numerous aspects of plant biology. Landmark studies connected the ATP-dependent ubiquitylation of substrates to their degradation by the 26S proteasome; however, nonproteolytic functions of the ubiquitin (Ub) code are also crucial to regulate protein interactions, activity, and localization. Regarding proteolytic functions of Ub, Lys-48-linked branched chains are the most common chain type for proteasomal degradation, whereas promotion of endocytosis and vacuolar degradation is triggered through monoubiquitylation or Lys63-linked chains introduced in integral or peripheral plasma membrane proteins. Hormone signaling relies on regulated protein turnover, and specifically the half-life of ABA signaling components is regulated both through the ubiquitin-26S proteasome system and the endocytic/vacuolar degradation pathway. E3 Ub ligases have been reported that target different ABA signaling core components, i.e., ABA receptors, PP2Cs, SnRK2s, and ABFs/ABI5 transcription factors. In this review, we focused specifically on the ubiquitylation of ABA receptors and PP2C coreceptors, as well as other post-translational modifications of ABA receptors (nitration and phosphorylation) that result in their ubiquitination and degradation.

An Update on Crop ABA Receptors

The hormone abscisic acid (ABA) orchestrates the plant stress response and regulates sophisticated metabolic and physiological mechanisms essential for survival in a changing environment. Plant ABA receptors were described more than 10 years ago, and a considerable amount of information is available for the model plant Arabidopsis thaliana. Unfortunately, this knowledge is still very limited in crops that hold the key to feeding a growing population. In this review, we summarize genomic, genetic and structural data obtained in crop ABA receptors. We also provide an update on ABA perception in major food crops, highlighting specific and common features of crop ABA receptors.

Control of ABA Signaling and Crosstalk with Other Hormones by the Selective Degradation of Pathway Components

A rapid and appropriate genetic and metabolic acclimation, which is crucial for plants' survival in a changing environment, is maintained due to the coordinated action of plant hormones and cellular degradation mechanisms influencing proteostasis. The plant hormone abscisic acid (ABA) rapidly accumulates in plants in response to environmental stress and plays a pivotal role in the reaction to various stimuli. Increasing evidence demonstrates a significant role of autophagy in controlling ABA signaling. This field has been extensively investigated and new discoveries are constantly being provided. We present updated information on the components of the ABA signaling pathway, particularly on transcription factors modified by different E3 ligases. Then, we focus on the role of selective autophagy in ABA pathway control and review novel evidence on the involvement of autophagy in different parts of the ABA signaling pathway that are important for crosstalk with other hormones, particularly cytokinins and brassinosteroids.

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.

OsCBE1, a Substrate Receptor of Cullin4-Based E3 Ubiquitin Ligase, Functions as a Regulator of Abiotic Stress Response and Productivity in Rice

Ubiquitination is an important environmental stress response, and E3 ubiquitin ligases play a major role in the process. T-DNA insertion mutants of rice, Oscbe1-1, and Oscbe1-2, were identified through the screening of cold stress tolerance at seedling stage. Oscbe1 mutants showed a significantly higher cold stress tolerance in the fresh weight, chlorophyll content, and photosynthetic efficiency than wild type. Molecular prediction showed that OsCBE1 (Oryza sativa Cullin4-Based E3 ubiquitin ligase1) encoded a novel substrate receptor of Cullin4-based E3 ubiquitin ligase complex (C4E3). Whereas Oscbe1 mutants had fewer panicles and grains than wild type in the paddy field, the overexpression lines of OsCBE1 had more panicles and grains, suggesting that OsCBE1 is involved in the regulation of both abiotic stress response and development. Oscbe1 mutants also showed ABA hypersensitivity during seed germination, suggesting OsCBE1 function for the stress response via ABA signaling. In silico analysis of OsCBE1 activity predicted a CCCH-type transcription factor, OsC3H32, as a putative substrate. Co-IP (Co-immunoprecipitation) study showed that OsCBE1 interacts with OsDDB1, an expected binding component of OsCBE1 and OsC3H32. Additionally, expression of OsOLE16, OsOLE18, and OsBURP5 were negatively related with expression of OsCBE1. These results suggest that OsCBE1 functions as a regulator of the abiotic stress response via CCCH as a member of the C4E3.

Grapevine U-Box E3 Ubiquitin Ligase VlPUB38 Negatively Regulates Fruit Ripening by Facilitating Abscisic-Aldehyde Oxidase Degradation

The plant U-box E3 ubiquitin ligase-mediated ubiquitin/26S proteasome degradation system plays a key role in plant growth and development. Previously identified as a member of the grape PUB gene family, PUB38 was shown to participate in the berry-ripening progress. Here, we demonstrate that the E3 ligase VlPUB38 mediates abscisic acid (ABA) synthesis via 26S proteasome degradation and its involvement in regulating fruit-ripening processes. Strawberry-overexpressing VlPUB38 lines displayed obvious inhibition of mature phenotype, and this was rescued by exogenous ABA treatment and MG132. Post-ABA treatment, expression levels of ABA response-related genes in VlPUB38-overexpressed Arabidopsis significantly exceeded controls. Strawberry and Arabidopsis ectopic expression assays suggest that VlPUB38 negatively regulates fruit ripening in an ABA-dependent manner. Moreover, VlPUB38 has ubiquitin ligase activity, which depends on the U-box-conserved domain. VlPUB38 interacts with abscisic-aldehyde oxidase (VlAAO), targeting VlAAO proteolysis via the 26S proteasome system. These results indicate that VlPUB38 negatively regulates grape fruit ripening by mediating the degradation of key factor VlAAO in the ABA synthesis pathway.

The AtMYB2 inhibits the formation of axillary meristem in Arabidopsis by repressing RAX1 gene under environmental stresses

AtMYB2 protein represses the formation of axillary meristems in response to environmental stresses so that plants can undergo a shorter vegetative development stage under environmental stresses. Shoot branching is an important event determined by endogenous factors during the development of plants. The formation of axillary meristem is also significantly repressed by environmental stresses and the underlying mechanism is largely unknown. The REGULATOR OF AXILLARY MERISTEMS (RAX) genes encode the R2R3 MYB transcription factors that have been shown to regulate the formation of axillary meristems in Arabidopsis. The AtMYB2 is also a member of R2R3 MYB gene family whose expression is usually induced by the environmental stresses. In this study, our results showed that AtMYB2 protein plays a pivotal negative regulatory role in the formation of axillary meristem. AtMYB2 is mainly expressed in the leaf axils as that of RAX1. The environmental stresses can increase the expression of AtMYB2 protein which further inhibits the expression of RAX1 gene by binding to its promoter. Therefore, AtMYB2 protein represses the formation of axillary meristems in response to environmental stresses so that plants can undergo a shorter vegetative development stage under environmental stresses.

AtPPRT3, a novel E3 ubiquitin ligase, plays a positive role in ABA signaling

KEY MESSAGE

The RING-type E3 ligase AtPPRT3 participates in the plant ABA responding as a positive regulator. E3 ubiquitin ligase, alike of classic plant stress resistance proteins, plays a vital role in regulating the degradation of stress-related proteins. In this study, we investigated the function of the RING-type E3 ubiquitin ligase AtPPRT3 in the ABA signaling pathway. AtPPRT3, located in the endoplasmic reticulum membrane, is involved in ABA signaling. The transcriptional expression of AtPPRT3 was induced by ABA, and the promoter region upstream of AtPPRT3 contains the ABA-responsive element (ABRE). Additionally, the β-glucuronidase (GUS) gene driven by the AtPPRT3 promoter was up-regulated in transgenic plants after ABA treated. We obtained AtPPRT3 function-deficient mutants atpprt3-1, atpprt3-2, and AtPPRT3 over-expressing lines (OE4 and OE5). In this study, atpprt3-1 and atpprt3-2 were less sensitive to exogenous ABA compared to Col-0, whereas OE4 and OE5 were more sensitive. Moreover, AtPPRT3 promotes ABA-mediated stomatal closure and inhibits water loss in Arabidopsis thaliana. After exogenous ABA treated, the transcriptional expression levels of AtDREB2A, AtKIN1, AtRD29A, AtERD10 and AtRD29B were up-regulated to greater extents in OEs and lower extents in atpprt3-1 and atpprt3-2 compared to Col-0. These results suggest that AtPPRT3 positively regulates ABA signaling in A. thaliana.

Interplay between the Ubiquitin Proteasome System and Ubiquitin-Mediated Autophagy in Plants

All eukaryotes rely on the ubiquitin-proteasome system (UPS) and autophagy to control the abundance of key regulatory proteins and maintain a healthy intracellular environment. In the UPS, damaged or superfluous proteins are ubiquitinated and degraded in the proteasome, mediated by three types of ubiquitin enzymes: E1s (ubiquitin activating enzymes), E2s (ubiquitin conjugating enzymes), and E3s (ubiquitin protein ligases). Conversely, in autophagy, a vesicular autophagosome is formed that transfers damaged proteins and organelles to the vacuole, mediated by a series of ATGs (autophagy related genes). Despite the use of two completely different componential systems, the UPS and autophagy are closely interconnected and mutually regulated. During autophagy, ATG8 proteins, which are autophagosome markers, decorate the autophagosome membrane similarly to ubiquitination of damaged proteins. Ubiquitin is also involved in many selective autophagy processes and is thus a common factor of the UPS and autophagy. Additionally, the components of the UPS, such as the 26S proteasome, can be degraded via autophagy, and conversely, ATGs can be degraded by the UPS, indicating cross regulation between the two pathways. The UPS and autophagy cooperate and jointly regulate homeostasis of cellular components during plant development and stress response.

Genome-wide identification and characterization of ABA receptor PYL gene family in rice

BACKGROUND

Abscisic acid (ABA), a key phytohormone that controls plant growth and stress responses, is sensed by the pyrabactin resistance 1(PYR1)/PYR1-like (PYL)/regulatory components of the ABA receptor (RCAR) family of proteins. Comprehensive information on evolution and function of PYL gene family in rice (Oryza sativa) needs further investigation. This study made detailed analysis on evolutionary relationship between PYL family members, collinearity, synteny, gene structure, protein motifs, cis-regulatory elements (CREs), SNP variations, miRNAs targeting PYLs and expression profiles in different tissues and stress responses.

RESULTS

Based on sequence homology with Arabidopsis PYL proteins, we identified a total of 13 PYLs in rice (BOP clade) and maize (PACCMAD clade), while other members of BOP (wheat - each diploid genome, barley and Brachypodium) and PACCMAD (sorghum and foxtail millet) have 8-9 PYLs. The phylogenetic analysis divided PYLs into three subfamilies that are structurally and functionally conserved across species. Gene structure and motif analysis of OsPYLs revealed that members of each subfamily have similar gene and motif structure. Segmental duplication appears be the driving force for the expansion of PYLs, and the majority of the PYLs underwent evolution under purifying selection in rice. 32 unique potential miRNAs that might target PYLs were identified in rice. Thus, the predicted regulation of PYLs through miRNAs in rice is more elaborate as compared with B. napus. Further, the miRNAs identified to in this study were also regulated by stresses, which adds additional layer of regulation of PYLs. The frequency of SAPs identified was higher in indica cultivars and were predominantly located in START domain that participate in ABA binding. The promoters of most of the OsPYLs have cis-regulatory elements involved in imparting abiotic stress responsive expression. In silico and q-RT-PCR expression analyses of PYL genes revealed multifaceted role of ABARs in shaping plant development as well as abiotic stress responses.

CONCLUSION

The predicted miRNA mediated regulation of OsPYLs and stress regulated expression of all OsPYLs, at least, under one stress, lays foundation for further validation and fine tuning ABA receptors for stress tolerance without yield penalty in rice.

Potato E3 ubiquitin ligase PUB27 negatively regulates drought tolerance by mediating stomatal movement

The ubiquitin-proteasome system (UPS) is one of the main ways of eukaryotic protein degradation and post-translational modification. It has proven as an essential process for plants to respond to abiotic stresses. Plant U-box (PUB) protein acts as a ubiquitin ligase, which recognizes and ubiquitinates the target proteins. Many PUBs have been involved in water stress in Arabidopsis and rice, but similar comprehensive studies in potato remained limited. In this study, the overexpressed and interfered transgenic potato plants of StPUB27 were obtained and their performances were evaluated under osmotic stress. The result showed that overexpression of StPUB27 accelerated the dehydration of detached leaves companied with greater stomatal conductance, while the down-regulated StPUB27 expression by RNA interference (RNAi) showed a smaller stomatal conductance and a lower rate of water loss in detached leaves, thus showing higher tolerance to osmotic stress. In addition, no significant changes in the proline content were observed between StPUB27 overexpressed and RNAi potato plants. The result demonstrated that potato E3 ubiquitin ligase PUB27 may negatively regulate drought tolerance by mediating stomatal conductance.

Ectopic Expression of OsPYL/RCAR7, an ABA Receptor Having Low Signaling Activity, Improves Drought Tolerance without Growth Defects in Rice

Overexpression of abscisic acid (ABA) receptors has been reported to enhance drought tolerance, but also to cause stunted growth and decreased crop yield. Here, we constructed transgenic rice for all monomeric ABA receptors and observed that only transgenic rice over-expressing OsPYL/RCAR7 showed similar phenotype with wild type, without total yield loss when grown under normal growth condition in a paddy field. Even though transgenic rice over-expressing OsPYL/RCAR7 showed neither an ABA-sensitivity nor an osmotic stress tolerance in plate assay, it showed drought tolerance. We investigated the ABA-dependent interaction with OsPP2CAs and ABA signaling induction by OsPYL/RCAR7. In yeast two hybrid assay, OsPYL/RCAR7 required critically higher ABA concentrations to interact with OsPP2CAs than other ABA receptors, and co-immunoprecipitation assay showed strong interaction under ABA treatment. When ABA-responsive signaling activity was monitored using a transient expression system in rice protoplasts, OsPYL/RCAR7 had the lowest ABA-responsive signaling activity as compared with other ABA receptors. OsPYL/RCAR7 also showed weak suppression of phosphatase activity as compared with other ABA receptors in vitro. Transcriptome analysis of transgenic rice over-expressing OsPYL/RCAR7 suggested that only a few genes were induced similar to control under without exogenous ABA, but a large number of genes was induced under ABA treatment compared with control. We conclude that OsPYL/RCAR7 is a novel functional ABA receptor that has low ABA signaling activity and exhibits high ABA dependence. These results lay the foundation for a new strategy to improve drought stress tolerance without compromising crop growth.

E3 ubiquitin ligase ATL61 acts as a positive regulator in abscisic acid mediated drought response in Arabidopsis

Abscisic acid (ABA) is an important plant hormone that mediates abiotic stresses in plant growth and development. A number of E3 ligases have been reported to be involved in ABA signaling pathway. In this study, we identified a C3H2C3 RING-type E3 ligase, Arabidopsis thaliana Tόxicos en Levadura 61 (ATL61), which regulated drought stress in planta. Enzyme assay in vitro demonstrated that ATL61 had E3 ubiquitin ligase activity, while point mutation of ATL61^{H109A, H122A} (mATL61) abolished its E3 ubiquitin ligase activity. ATL61 overexpression plants exhibited ABA hypersensitivity and were more tolerant to drought, while the atl61 mutant plants were insensitive to ABA. Moreover, mATL61 overexpression lines exhibited similar ABA-related phenotypes with wild type (WT) plants. The transcript abundances of ABA-mediated drought stress-related genes RD20 and RD22 were higher in ATL61 overexpression plants than those in WT, atl61, and mATL61 plants. Our results indicated that ATL61 acted as a positive regulator in the ABA-mediated drought stress response.

Agronomic, physiological and molecular characterisation of rice mutants revealed the key role of reactive oxygen species and catalase in high-temperature stress tolerance

Climatic variations have increased the occurrence of heat stress during critical growth stages, which negatively affects grain yield in rice. Plants adapt to harsh environments, and particularly high-temperature stress, by regulating their physiological and biochemical processes, which are key tolerance mechanisms. The identification of heat-tolerant rice genotypes and reliable selection indices are crucial for rice improvement programs. Here, we evaluated the response of a rice mutant population for high-temperature stress at the seedling and reproductive stages based on agronomic, physiological and molecular indices. Estimates of variance components revealed significant differences (P < 0.001) among genotypes, treatments and their interactions for almost all traits. The principal component analysis showed significant diversity among genotypes and traits under high-temperature stress. The mutant HTT-121 was identified as the most heat-tolerant mutant with higher grain yield, panicle fertility, cell membrane thermo-stability (CMTS) and antioxidant enzyme levels under heat stress. Various seedling-based morpho-physiological traits (leaf fresh weight, relative water contents, malondialdehyde, CMTS) and biochemical traits (superoxide dismutase, catalase and hydrogen peroxide) explained variations in grain yield that could be used as selection indices for heat tolerance in rice during early growth. Notably, heat-sensitive mutants accumulated reactive oxygen species, reduced catalase activity and upregulated OsSRFP1 expression under heat stress, suggesting their key roles in regulating heat tolerance in rice. The heat-tolerant mutants identified in this study could be used in breeding programs and to develop mapping populations to unravel the underlying genetic architecture for heat-stress adaptability.

RBR-Type E3 Ligases and the Ubiquitin-Conjugating Enzyme UBC26 Regulate Abscisic Acid Receptor Levels and Signaling

The turnover of abscisic acid (ABA) signaling core components modulates the plant's response to ABA and is regulated by ubiquitination. We show that Arabidopsis (Arabidopsis thaliana) RING Finger ABA-Related1 (RFA1) and RFA4 E3 ubiquitin ligases, members of the RING between RING fingers (RBR)-type RSL1/RFA family, are key regulators of ABA receptor stability in root and leaf tissues, targeting ABA receptors for degradation in different subcellular locations. RFA1 is localized both in the nucleus and cytosol, whereas RFA4 shows specific nuclear localization and promotes nuclear degradation of ABA receptors. Therefore, members of the RSL1/RFA family interact with ABA receptors at plasma membrane, cytosol, and nucleus, targeting them for degradation via the endosomal/vacuolar RSL1-dependent pathway or 26S proteasome. Additionally, we provide insight into the physiological function of the relatively unexplored plant RBR-type E3 ligases, and through mutagenesis and biochemical assays we identified cysteine-361 in RFA4 as the putative active site cysteine, which is a distinctive feature of RBR-type E3 ligases. Endogenous levels of PYR1 and PYL4 ABA receptors were higher in the rfa1 rfa4 double mutant than in wild-type plants. UBC26 was identified as the cognate nuclear E2 enzyme that interacts with the RFA4 E3 ligase and forms UBC26-RFA4-receptor complexes in nuclear speckles. Loss-of-function ubc26 alleles and the rfa1 rfa4 double mutant showed enhanced sensitivity to ABA and accumulation of ABA receptors compared with the wild type. Together, our results reveal a sophisticated mechanism by which ABA receptors are targeted by ubiquitin at different subcellular locations, in which the complexity of the ABA receptor family is mirrored in the partner RBR-type E3 ligases.

Rice OsHSFA3 Gene Improves Drought Tolerance by Modulating Polyamine Biosynthesis Depending on Abscisic Acid and ROS Levels

Drought is a serious problem, which causes heavy yield losses for rice. Heat-shock factors (HSFs) had been implicated in tolerance to drought and high temperature. However, there has not been much functional characterization and mechanism clarification in rice. Previously, we found an HSF gene, OsHSFA3, was highly related with drought tolerance after screening from 10,000 different samples. Herein, we cloned the OsHSFA3 from rice and overexpressed it in Arabidopsis thaliana to study its regulatory mechanism of drought tolerance. Phenotypic and physiological assays of the transgenic Arabidopsis lines showed that overexpression of OsHSFA3 confers drought tolerance by reducing water loss and reactive oxygen species (ROS) levels, whereas it increases abscisic acid (ABA) levels. However, enzymatic antioxidants such as activity levels of superoxide dismutase, peroxidase and catalase were not significantly different between wild type and transgenic lines. Instead, we observed a significant increase in polyamine content, which was correlated with increased AtADC1, AtADC2, SPDS1 and SPMS expression levels. In silico and in vivo analyses confirmed that OsHSFA3 is a nuclear-localized gene. In addition, OsHSFA3 can bind to the promoter of AtADC1 and OsADC via a yeast one-hybrid assay. Overall, this study reveals that OsHSFA3 improves drought tolerance in Arabidopsis not only by increasing ABA levels, but also by modulating polyamine levels to maintain ROS homeostasis, therefore it could be a strong candidate to develop drought-tolerant rice cultivars.