The single-subunit RING-type E3 ubiquitin ligase RSL1 targets PYL4 and PYR1 ABA receptors in plasma membrane to modulate abscisic acid signaling

Modulation of abscisic acid signaling via endosomal TOL proteins

The phytohormone abscisic acid (ABA) functions in the control of plant stress responses, particularly in drought stress. A significant mechanism in attenuating and terminating ABA signals involves regulated protein turnover, with certain ABA receptors, despite their main presence in the cytosol and nucleus, subjected to vacuolar degradation via the Endosomal Sorting Complex Required for Transport (ESCRT) machinery. Collectively our findings show that discrete TOM1-LIKE (TOL) proteins, which are functional ESCRT-0 complex substitutes in plants, affect the trafficking for degradation of core components of the ABA signaling and transport machinery. TOL2,3,5 and 6 modulate ABA signaling where they function additively in degradation of ubiquitinated ABA receptors and transporters. TOLs colocalize with their cargo in different endocytic compartments in the root epidermis and in guard cells of stomata, where they potentially function in ABA-controlled stomatal aperture. Although the tol2/3/5/6 quadruple mutant plant line is significantly more drought-tolerant and has a higher ABA sensitivity than control plant lines, it has no obvious growth or development phenotype under standard conditions, making the TOL genes ideal candidates for engineering to improved plant performance.

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.

Stress response membrane protein OsSMP2 negatively regulates rice tolerance to drought

In a gene chip analysis, rice (Oryza sativa) OsSMP2 gene expression was induced under various abiotic stresses, prompting an investigation into its role in drought resistance and abscisic acid signaling. Subsequent experiments, including qRT-PCR and β-glucuronidase activity detection, affirmed the OsSMP2 gene's predominant induction by drought stress. Subcellular localization experiments indicated the OsSMP2 protein primarily localizes to the cell membrane system. Overexpressing OsSMP2 increased sensitivity to exogenous abscisic acid, reducing drought resistance and leading to reactive oxygen species accumulation under drought stress. Conversely, in simulated drought experiments, OsSMP2-silenced transgenic plants showed significantly longer roots compared with the wild-type Nipponbare. These results suggest that OsSMP2 overexpression negatively affects rice drought resistance, offering valuable insights into molecular mechanisms, and highlight OsSMP2 as a potential target for enhancing crop resilience to drought stress.

Potato E3 ubiquitin ligase StRFP1 positively regulates late blight resistance by degrading sugar transporters StSWEET10c and StSWEET11

Potato (Solanum tuberosum) is the fourth largest food crop in the world. Late blight, caused by oomycete Phytophthora infestans, is the most devastating disease threatening potato production. Previous research has shown that StRFP1, a potato Arabidopsis Tóxicos en Levadura (ATL) family protein, positively regulates late blight resistance via its E3 ligase activity. However, the underlying mechanism is unknown. Here, we reveal that StRFP1 is associated with the plasma membrane (PM) and undergoes constitutive endocytic trafficking. Its PM localization is essential for inhibiting P. infestans colonization. Through in vivo and in vitro assays, we investigated that StRFP1 interacts with two sugar transporters StSWEET10c and StSWEET11 at the PM. Overexpression (OE) of StSWEET10c or StSWEET11 enhances P. infestans colonization. Both StSWEET10c and StSWEET11 exhibit sucrose transport ability in yeast, and OE of StSWEET10c leads to an increased sucrose content in the apoplastic fluid of potato leaves. StRFP1 ubiquitinates StSWEET10c and StSWEET11 to promote their degradation. We illustrate a novel mechanism by which a potato ATL protein enhances disease resistance by degrading susceptibility (S) factors, such as Sugars Will Eventually be Exported Transporters (SWEETs). This offers a potential strategy for improving disease resistance by utilizing host positive immune regulators to neutralize S factors.

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.

Role of Abscisic Acid, Reactive Oxygen Species, and Ca2+ Signaling in Hydrotropism-Drought Avoidance-Associated Response of Roots

Plant roots exert hydrotropism in response to moisture gradients to avoid drought stress. The regulatory mechanism underlying hydrotropism involves novel regulators such as MIZ1 and GNOM/MIZ2 as well as abscisic acid (ABA), reactive oxygen species (ROS), and Ca2+ signaling. ABA, ROS, and Ca2+ signaling are also involved in plant responses to drought stress. Although the mechanism of moisture gradient perception remains largely unknown, the sensory apparatus has been reported to reside in the root elongation zone rather than in the root cap. In Arabidopsis roots, hydrotropism is mediated by the action of MIZ1 and ABA in the cortex of the elongation zone, the accumulation of ROS at the root curvature, and the variation in the cytosolic Ca2+ concentration in the entire root tip including the root cap and stele of the elongation zone. Moreover, root exposure to moisture gradients has been proposed to cause asymmetric ABA distribution or Ca2+ signaling, leading to the induction of the hydrotropic response. A comprehensive and detailed analysis of hydrotropism regulators and their signaling network in relation to the tissues required for their function is apparently crucial for understanding the mechanisms unique to root hydrotropism. Here, referring to studies on plant responses to drought stress, we summarize the recent findings relating to the role of ABA, ROS, and Ca2+ signaling in hydrotropism, discuss their functional sites and plausible networks, and raise some questions that need to be answered in future studies.

Integrating multi-omics data reveals energy and stress signaling activated by abscisic acid in Arabidopsis

Phytohormones are essential signaling molecules regulating various processes in growth, development, and stress responses. Genetic and molecular studies, especially using Arabidopsis thaliana (Arabidopsis), have discovered many important players involved in hormone perception, signal transduction, transport, and metabolism. Phytohormone signaling pathways are extensively interconnected with other endogenous and environmental stimuli. However, our knowledge of the huge and complex molecular network governed by a hormone remains limited. Here we report a global overview of downstream events of an abscisic acid (ABA) receptor, REGULATORY COMPONENTS OF ABA RECEPTOR (RCAR) 6 (also known as PYRABACTIN RESISTANCE 1 [PYR1]-LIKE [PYL] 12), by integrating phosphoproteomic, proteomic and metabolite profiles. Our data suggest that the RCAR6 overexpression constitutively decreases the protein levels of its coreceptors, namely clade A protein phosphatases of type 2C, and activates sucrose non-fermenting-1 (SNF1)-related protein kinase 1 (SnRK1) and SnRK2, the central regulators of energy and ABA signaling pathways. Furthermore, several enzymes in sugar metabolism were differentially phosphorylated and expressed in the RCAR6 line, and the metabolite profile revealed altered accumulations of several organic acids and amino acids. These results indicate that energy- and water-saving mechanisms mediated by the SnRK1 and SnRK2 kinases, respectively, are under the control of the ABA receptor-coreceptor complexes.

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.

BcABF1 Plays a Role in the Feedback Regulation of Abscisic Acid Signaling via the Direct Activation of BcPYL4 Expression in Pakchoi

Abscisic acid-responsive element-binding factor 1 (ABF1), a key transcription factor in the ABA signal transduction process, regulates the expression of downstream ABA-responsive genes and is involved in modulating plant responses to abiotic stress and developmental processes. However, there is currently limited research on the feedback regulation of ABF1 in ABA signaling. This study delves into the function of BcABF1 in Pakchoi. We observed a marked increase in BcABF1 expression in leaves upon ABA induction. The overexpression of BcABF1 not only spurred Arabidopsis growth but also augmented the levels of endogenous IAA. Furthermore, BcABF1 overexpression in Arabidopsis significantly decreased leaf water loss and enhanced the expression of genes associated with drought tolerance in the ABA pathway. Intriguingly, we found that BcABF1 can directly activate BcPYL4 expression, a critical receptor in the ABA pathway. Similar to BcABF1, the overexpression of BcPYL4 in Arabidopsis also reduces leaf water loss and promotes the expression of drought and other ABA-responsive genes. Finally, our findings suggested a novel feedback regulation mechanism within the ABA signaling pathway, wherein BcABF1 positively amplifies the ABA signal by directly binding to and activating the BcPYL4 promoter.

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 identification and characterization of the RZFP gene family and analysis of its expression pattern under stress in Populus trichocarpa

Forest trees face many abiotic stressors during their lifetime, including drought, heavy metals, high salinity, and chills, affecting their quality and yield. The RING-type ubiquitin ligase E3 is an invaluable component of the ubiquitin-proteasome system (UPS) and participates in plant growth and environmental interactions. Interestingly, only a few studies have explored the RING ZINC FINGER PROTEIN (RZFP) gene family. This study identified eight PtrRZFPs genes in the Populus genome, and their molecular features were analyzed. Gene structure analysis revealed that all PtrRZFPs genes contained >10 introns. Evolutionarily, the RZFPs were separated into four categories, and segmental replication events facilitated their amplification. Notably, many stress-related elements have been identified in the promoters of PtrRZFPs using Cis-acting element analysis. Moreover, some PtrRZFPs were significantly induced by drought and sorbitol, revealing their potential roles in regulating stress responses. Particularly, overexpression of the PtrRZFP1 gene in poplars conferred excellent drought tolerance; however, PtrRZFP1 knockdown plants were drought-sensitive. We identified the potential upstream transcription factors of PtrRZFPs and revealed the possible biological functions of RZFP1/4/7 in resisting osmotic and salt stress, laying the foundation for subsequent biological function studies and providing genetic resources for genetic engineering breeding for drought resistance in forest trees. This study offers crucial information for the further exploration of the functions of RZFPs in poplars.

Seed Longevity and Ageing: A Review on Physiological and Genetic Factors with an Emphasis on Hormonal Regulation

Upon storage, seeds inevitably age and lose their viability over time, which determines their longevity. Longevity correlates with successful seed germination and enhancing this trait is of fundamental importance for long-term seed storage (germplasm conservation) and crop improvement. Seed longevity is governed by a complex interplay between genetic factors and environmental conditions experienced during seed development and after-ripening that will shape seed physiology. Several factors have been associated with seed ageing such as oxidative stress responses, DNA repair enzymes, and composition of seed layers. Phytohormones, mainly abscisic acid, auxins, and gibberellins, have also emerged as prominent endogenous regulators of seed longevity, and their study has provided new regulators of longevity. Gaining a thorough understanding of how hormonal signalling genes and pathways are integrated with downstream mechanisms related to seed longevity is essential for formulating strategies aimed at preserving seed quality and viability. A relevant aspect related to research in seed longevity is the existence of significant differences between results depending on the seed equilibrium relative humidity conditions used to study seed ageing. Hence, this review delves into the genetic, environmental and experimental factors affecting seed ageing and longevity, with a particular focus on their hormonal regulation. We also provide gene network models underlying hormone signalling aimed to help visualize their integration into seed longevity and ageing. We believe that the format used to present the information bolsters its value as a resource to support seed longevity research for seed conservation and crop improvement.

Dry side of the core: a meta-analysis addressing the original nature of the ABA signalosome at the onset of seed imbibition

The timing of seedling emergence is a major agricultural and ecological fitness trait, and seed germination is controlled by a complex molecular network including phytohormone signalling. One such phytohormone, abscisic acid (ABA), controls a large array of stress and developmental processes, and researchers have long known it plays a crucial role in repressing germination. Although the main molecular components of the ABA signalling pathway have now been identified, the molecular mechanisms through which ABA elicits specific responses in distinct organs is still enigmatic. To address the fundamental characteristics of ABA signalling during germination, we performed a meta-analysis focusing on the Arabidopsis dry seed proteome as a reflexion basis. We combined cutting-edge proteome studies, comparative functional analyses, and protein interaction information with genetic and physiological data to redefine the singular composition and operation of the ABA core signalosome from the onset of seed imbibition. In addition, we performed a literature survey to integrate peripheral regulators present in seeds that directly regulate core component function. Although this may only be the tip of the iceberg, this extended model of ABA signalling in seeds already depicts a highly flexible system able to integrate a multitude of information to fine-tune the progression of germination.

The RING-Finger Protein NbRFP1 Contributes to Regulating the Host Hypersensitive Response Induced by Oat Dwarf Virus RepA

Our previous study identified that the RepA protein encoded by the oat dwarf virus (ODV) was responsible for inducing a strong hypersensitive response (HR) during the virus infection in non-host tobacco plants. However, little was known about the molecular mechanism of the RepA-elicited HR. Here, a RING-finger protein, which is described as NbRFP1 and is mainly located in the cytoplasm and nucleus in Nicotiana benthamiana cells, was confirmed to interact with RepA. In addition, the accumulation level of NbRFP1 in N. benthamiana leaves was enhanced by either ODV infection or by only RepA expression. The knockdown of NbRFP1 by a TRV-mediated virus-induced gene silencing markedly delayed the ODV or RepA-elicited HR. By contrast, the overexpression of NbRFP1 in N. benthamiana conferred enhanced resistance to ODV infection and promoted RepA-induced HR. Further mutation analysis showed that a RING-finger domain located in NbRFP1 plays important roles in modulating RepA-induced HR, as well as in mediating the interaction between NbRFP1 and RepA.

The NAC transcription factor MdNAC4 positively regulates nitrogen deficiency-induced leaf senescence by enhancing ABA biosynthesis in apple

Although it is well established that nitrogen (N) deficiency induces leaf senescence, the molecular mechanism of N deficiency-induced leaf senescence remains largely unknown. Here, we show that an abscisic acid (ABA)-responsive NAC transcription factor (TF) is involved in N deficiency-induced leaf senescence. The overexpression of MdNAC4 led to increased ABA levels in apple calli by directly activating the transcription of the ABA biosynthesis gene MdNCED2. In addition, MdNAC4 overexpression promoted N deficiency-induced leaf senescence. Further investigation showed that MdNAC4 directly bound the promoter of the senescence-associated gene (SAG) MdSAG39 and upregulated its expression. Interestingly, the function of MdNAC4 in promoting N deficiency-induced leaf senescence was enhanced in the presence of ABA. Furthermore, we identified an interaction between the ABA receptor protein MdPYL4 and the MdNAC4 protein. Moreover, MdPYL4 showed a function similar to that of MdNAC4 in ABA-mediated N deficiency-induced leaf senescence. These findings suggest that ABA plays a central role in N deficiency-induced leaf senescence and that MdPYL4 interacts with MdNAC4 to enhance the response of the latter to N deficiency, thus promoting N deficiency-induced leaf senescence. In conclusion, our results provide new insight into how MdNAC4 regulates N deficiency-induced leaf senescence.

Bacterial Volatiles (mVOC) Emitted by the Phytopathogen Erwinia amylovora Promote Arabidopsis thaliana Growth and Oxidative Stress

Phytopathogens are well known for their devastating activity that causes worldwide significant crop losses. However, their exploitation for crop welfare is relatively unknown. Here, we show that the microbial volatile organic compound (mVOC) profile of the bacterial phytopathogen, Erwinia amylovora, enhances Arabidopsis thaliana shoot and root growth. GC-MS head-space analyses revealed the presence of typical microbial volatiles, including 1-nonanol and 1-dodecanol. E. amylovora mVOCs triggered early signaling events including plasma transmembrane potential Vm depolarization, cytosolic Ca2+ fluctuation, K+-gated channel activity, and reactive oxygen species (ROS) and nitric oxide (NO) burst from few minutes to 16 h upon exposure. These early events were followed by the modulation of the expression of genes involved in plant growth and defense responses and responsive to phytohormones, including abscisic acid, gibberellin, and auxin (including the efflux carriers PIN1 and PIN3). When tested, synthetic 1-nonanol and 1-dodecanol induced root growth and modulated genes coding for ROS. Our results show that E. amylovora mVOCs affect A. thaliana growth through a cascade of early and late signaling events that involve phytohormones and ROS.

CRISPR/Cas9 Gene Editing of NtAITRs, a Family of Transcription Repressor Genes, Leads to Enhanced Drought Tolerance in Tobacco

Tobacco is a cash crop throughout the world, and its growth and development are affected by abiotic stresses including drought stress; therefore, drought-tolerant breeding may help to improve tobacco yield and quality under drought stress conditions. Considering that the plant hormone ABA (abscisic acid) is able to regulate plant responses to abiotic stresses via activating ABA response genes, the characterization of ABA response genes may enable the identification of genes that can be used for molecular breeding to improve drought tolerance in tobacco. We report here the identification of NtAITRs (Nicotiana tabacum ABA-induced transcription repressors) as a family of novel regulators of drought tolerance in tobacco. Bioinformatics analysis shows that there are a total of eight NtAITR genes in tobacco, and all the NtAITRs have a partially conserved LxLxL motif at their C-terminus. RT-PCR results show that the expression levels of at least some NtAITRs were increased in response to ABA and drought treatments, and NtAITRs, when recruited to the Gal4 promoter via a fused GD (Gal4 DNA-binding domain), were able to repress transcription activator LD-VP activated expression of the LexA-Gal4-GUS reporter gene. Roles of NtAITRs in regulating drought tolerance in tobacco were analyzed by generating CRISPR/Cas9 gene-edited mutants. A total of three Cas9-free ntaitr12356 quintuple mutants were obtained, and drought treatment assays show that drought tolerance was increased in the ntaitr12356 quintuple mutants. On the other hand, results of seed germination and seedling greening assays show that ABA sensitivity was increased in the ntaitr12356 quintuple mutants, and the expression levels of some ABA signaling key regulator genes were altered in the ntaitr12356-c3 mutant. Taken together, our results suggest that NtAITRs are ABA-responsive genes, and that NtAITRs function as transcription repressors and negatively regulate drought tolerance in tobacco, possibly by affecting plant ABA response via affecting the expression of ABA signaling key regulator genes.

The interaction of ABA and ROS in plant growth and stress resistances

The plant hormone ABA (abscisic acid) plays an extremely important role in plant growth and adaptive stress, including but are not limited to seed germination, stomatal closure, pathogen infection, drought and cold stresses. Reactive oxygen species (ROS) are response molecules widely produced by plant cells under biotic and abiotic stress conditions. The production of apoplast ROS is induced and regulated by ABA, and participates in the ABA signaling pathway and its regulated plant immune system. In this review, we summarize ABA and ROS in apoplast ROS production, plant response to biotic and abiotic stresses, plant growth regulation, ABA signal transduction, and the regulatory relationship between ABA and other plant hormones. In addition, we also discuss the effects of protein post-translational modifications on ABA and ROS related factors.

Functional characterization of E3 ubiquity ligase Bra015092 in pollen development of Brassica campestris ssp. Chinensis

Pollen development plays an important role in the sexual reproduction of seed-type plants. Ubiquitination of proteins is an essential link in the post-translational modification of proteins. E3 ubiquity ligase is a key protein that recognizes substrates in the protein ubiquitination pathway. The hybrid line "Bcajh97-01A/B" of Chinese cabbage (Brassica campestris L. ssp. Chinensis) was used as test material. The gene Bra015092, with a size of 642 bp, was amplified. Semi-quantitative (RT-PCR) and quantitative real-time PCR (qRT-PCR) techniques were utilized to analyze the expression of Bra015092 in the dual-purpose line of Chinese cabbage. It was found that Bra015092 had a higher expression level in inflorescence. Subcellular localization analysis showed that Bra015092 and GFP fusion expression protein widely exist in tobacco epidermal cells. Bra015092 was transformed into "Youqing49" cabbage to obtain Bra015092^OE overexpressing transgenic lines. The morphological observation of Bra015092^OE plants showed that the pollen of BcMF29^OE plants became deformed and inactive, and the vegetative and reproductive nuclei were abnormally developed. The in vitro germination experiments showed that about 24.5% of the pollen in Bra015092^OE plants could not germinate. The results of the semi-thin section showed that the pollen development of Bra015092^OE plants was abnormal at the stage of binuclear pollen grains. Transmission electron microscopy revealed that the pollen grains of Bra015092^OE plants gradually degraded from the binuclear to the trinucleate pollen grain stage, and the pollen inner wall was abnormally developed, indicating that Bra015092 plays a major role in the process of pollen development.

Arabidopsis thaliana E3 ligase AIRP4 is involved in GA synthesis

Arabidopsis abscisic acid ABA-Insensitive RING Proteins (AtAIRP1-4) are RING E3s that play significant roles in ABA-signaling pathways. However, it is still unclear whether they have other functions. Here, AtAIRP4 was determined to play a role in response to gibberellin A3 (GA₃) in Arabidopsis thaliana. After proAtAIRP4::GUS transgenic lines were treated with GA₃, the GUS activity decreased in hypocotyls. Increased hypocotyl elongation in response to GA₃ seen in WT was not observed in the AtAIRP4-overexpression lines, whereas AtAIRP4-overexpression lines were hypersensitive to Paclobutrazol (PAC, an inhibitor of GA biosynthesis) during the seed germination stage. Additionally, AtAIRP4-overexpressing lines showed the lowest level of primary root elongation in the presence of GA₃. The levels of endogenous GA₃ in 35S::AtAIRP4 lines were lower than those in wild-type. In addition, among the plants, the mRNA levels of the GA synthetic gene GIBBERELLIN 20-OXIDASE1 (GA20ox1) was the lowest in overexpressing line. However, the expression of the response gene DELLA RGA-LIKE3 (RGL3) was the highest in overexpressing lines after treatment with GA₃. Thus, AtAIRP4 plays a negative role in GA-mediated hypocotyl elongation and root growth, and it inhibits the synthesis of endogenous biologically active GA₃ to some extent.

The key clock component ZEITLUPE (ZTL) negatively regulates ABA signaling by degradation of CHLH in Arabidopsis

Ubiquitination-mediated protein degradation plays important roles in ABA signal transduction and delivering responses to chloroplast stress signals in plants, but additional E3 ligases of protein ubiquitination remain to be identified to understand the complex signaling network. Here we reported that ZEITLUPE (ZTL), an F-box protein, negatively regulates abscisic acid (ABA) signaling during ABA-inhibited early seedling growth and ABA-induced stomatal closure in Arabidopsis thaliana. Using molecular biology and biochemistry approaches, we demonstrated that ZTL interacts with and ubiquitinates its substrate, CHLH/ABAR (Mg-chelatase H subunit/putative ABA receptor), to modulate CHLH stability via the 26S proteasome pathway. CHLH acts genetically downstream of ZTL in ABA and drought stress signaling. Interestingly, ABA conversely induces ZTL phosphorylation, and high levels of ABA also induce CHLH proteasomal degradation, implying that phosphorylated ZTL protein may enhance the affinity to CHLH, leading to the increased degradation of CHLH after ABA treatment. Taken together, our results revealed a possible mechanism of reciprocal regulation between ABA signaling and the circadian clock, which is thought to be essential for plant fitness and survival.

MLKs kinases phosphorylate the ESCRT component FREE1 to suppress abscisic acid sensitivity of seedling establishment

The FYVE domain protein required for endosomal sorting 1 (FREE1), which was previously identified as a plant-specific component of the endosomal sorting complex required for transport machinery, plays an essential role in endosomal trafficking. Moreover, FREE1 also functions as an important negative regulator in abscisic acid (ABA) signalling. Multiple phosphorylations and ubiquitination sites have been identified in FREE1, hence unveiling the factors involved in posttranslational regulation of FREE1 is critical for comprehensively understanding FREE1-related regulatory networks during plant growth. Here, we demonstrate that plant-specific casein kinase I members MUT9-like kinases 1-4 (MLKs 1-4)/Arabidopsis EL1-like 1-4 interact with and phosphorylate FREE1 at serine residue S582, thereby modulating the nuclear accumulation of FREE1. Consequently, mutation of S582 to non-phosphorylable residue results in reduced nuclear localization of FREE1 and enhanced ABA response. In addition, mlk123 and mlk134 triple mutants accumulate less FREE1 in the nucleus and display hypersensitive responses to ABA treatment, whereas overexpression of the nuclear-localized FREE1 can restore the ABA sensitivity of seedling establishment in mlks triple mutants. Collectively, our study demonstrates a previously unidentified function of MLKs in attenuating ABA signalling in the nucleus by regulating the phosphorylation and nuclear accumulation of FREE1.

Orphan gene PpARDT positively involved in drought tolerance potentially by enhancing ABA response in Physcomitrium (Physcomitrella) patens

Almost all genomes have orphan genes, the majority of which are not functionally annotated. There is growing evidence showed that orphan genes may play important roles in the environmental stress response of Physcomitrium patens. We identified PpARDT (ABA-responsive drought tolerance) as a moss-specific and ABA-responsive orphan gene in P. patens. PpARDT is mainly expressed during the gametophytic stage of the life cycle, and the expression was induced by different abiotic stresses. A PpARDT knockout (Ppardt) mutant showed reduced dehydration-rehydration tolerance, and the phenotype could be rescued by exogenous ABA. Meanwhile, transgenic Arabidopsis lines exhibiting heterologous expression of PpARDT were more sensitive to exogenous ABA than wild-type (Col-0) plants and showed enhanced drought tolerance. These indicate that PpARDT confers drought tolerance among land plants potentially by enhancing ABA response. Further, we identified genes encoding abscisic acid receptor PYR/PYL family proteins, and ADP-ribosylation factors (Arf) as hub genes associated with the Ppardt phenotype. Given the lineage-specific characteristics of PpARDT, our results provide insights into the roles of orphan gene in shaping lineage-specific adaptation possibly by recruiting common pre-existed pathway components.

Brassinosteroid-Insensitive 1-Associated Receptor Kinase 1 Modulates Abscisic Acid Signaling by Inducing PYR1 Monomerization and Association With ABI1 in Arabidopsis

Brassinosteroid-Insensitive 1-Associated Receptor Kinase 1 (BAK1) is a versatile kinase involved in many different plant developmental responses. Previously, we showed that BAK1 interacts with open stomata 1 (OST1), a cytoplasmic kinase, to promote abscisic acid (ABA)-induced stomatal closure. ABA is a plant hormone that primarily regulates stress responses and is recognized by the PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENT OF ABA RECEPTORS (RCAR), which activates ABA signaling. Here, we demonstrated that BAK1 interacts with PYR1 and phosphorylates PYR1 in response to ABA in plants. We identified T137 and S142 of PYR1 as the phosphosites targeted by BAK1. Using phosphomimetic (PYR1DD) and phospho-dead (PYR1AA) PYR1 compared with wild-type PYR1, we showed that transgenic plants overexpressing a phosphomimetic PYR1 exhibited hypersensitivity to the inhibition of ABA-induced root growth and seed germination and increased ABA-induced stomatal closure and ABA-inducible gene expression. As underlying reasons for these phenomena, we further demonstrated that phosphorylated PYR1 existed in a monomeric form, in which ABA binding was increased, and the degree of complex formation with ABI1 was also increased. These results suggest that BAK1 positively modulates ABA signaling through interaction with PYR1, in addition to OST1.

The ABI3 Transcription Factor Interaction and Antagonism with Ubiquitin E3 Ligase ScPRT1 in Syntrichia caninervis

The ubiquitination pathway has been found to regulate plant responses to environmental stress. However, the role of E3 ubiquitin ligase in desiccation tolerant moss has not yet been elucidated. Previous research has shown that the abscisic acid (ABA) signaling factor ScABI3 can significantly increase desiccation tolerance and reduce ABA sensitivity in the desert moss Syntrichia caninervis. In this study, we identified a RING-type E3 ubiquitin ligase, ScPRT1, and showed that ScABI3 can directly interact with ScPRT1 in vitro and in vivo. Furthermore, we found that the high expression of ScPRT1 can interfere with the transcription of ScABI3 under ABA treatment. Therefore, we speculate that ScPRT1 may degrade ScABI3 through the ubiquitin-26S proteasome system and participate in ABA-dependent signaling in response to ABA-insensitivity or desiccation tolerance in S. caninervis. The findings from our study may enrich our knowledge of the role of E3 ubiquitin ligase in desiccation tolerance and lay a theoretical foundation for an in-depth study of the relationship between ubiquitination modification and ABA signal transduction under environmental stress.

The deubiquitinases UBP12 and UBP13 integrate with the E3 ubiquitin ligase XBAT35.2 to modulate VPS23A stability in ABA signaling

Ubiquitination-mediated protein degradation in both the 26S proteasome and vacuole is an important process in abscisic acid (ABA) signaling. However, the role of deubiquitination in this process remains elusive. Here, we demonstrate that two deubiquitinating enzymes (DUBs), ubiquitin-specific protease 12 (UBP12) and UBP13, modulate ABA signaling and drought tolerance by deubiquitinating and stabilizing the endosomal sorting complex required for transport-I (ESCRT-I) component vacuolar protein sorting 23A (VPS23A) and thereby affect the stability of ABA receptors in Arabidopsis thaliana. Genetic analysis showed that VPS23A overexpression could rescue the ABA hypersensitive and drought tolerance phenotypes of ubp12-2w or ubp13-1. In addition to the direct regulation of VPS23A, we found that UBP12 and UBP13 also stabilized the E3 ligase XB3 ortholog 5 in A. thaliana (XBAT35.2) in response to ABA treatment. Hence, we demonstrated that UBP12 and UBP13 are previously unidentified rheostatic regulators of ABA signaling and revealed a mechanism by which deubiquitination precisely monitors the XBAT35/VPS23A ubiquitination module in the ABA response.

Abscisic Acid Machinery Is under Circadian Clock Regulation at Multiple Levels

Abscisic acid (ABA) is recognized as the key hormonal regulator of plant stress physiology. This phytohormone is also involved in plant growth and development under normal conditions. Over the last 50 years the components of ABA machinery have been well characterized, from synthesis to molecular perception and signaling; knowledge about the fine regulation of these ABA machinery components is starting to increase. In this article, we review a particular regulation of the ABA machinery that comes from the plant circadian system and extends to multiple levels. The circadian clock is a self-sustained molecular oscillator that perceives external changes and prepares plants to respond to them in advance. The circadian system constitutes the most important predictive homeostasis mechanism in living beings. Moreover, the circadian clock has several output pathways that control molecular, cellular and physiological downstream processes, such as hormonal response and transcriptional activity. One of these outputs involves the ABA machinery. The circadian oscillator components regulate expression and post-translational modification of ABA machinery elements, from synthesis to perception and signaling response. The circadian clock establishes a gating in the ABA response during the day, which fine tunes stomatal closure and plant growth response.

Interactome of Arabidopsis Thaliana

More than 95,000 protein–protein interactions of Arabidopsis thaliana have been published and deposited in databases. This dataset was supplemented by approximately 900 additional interactions, which were identified in the literature from the years 2002–2021. These protein–protein interactions were used as the basis for a Cytoscape network and were supplemented with data on subcellular localization, gene ontologies, biochemical properties and co-expression. The resulting network has been exemplarily applied in unraveling the PPI-network of the plant vacuolar proton-translocating ATPase (V-ATPase), which was selected due to its central importance for the plant cell. In particular, it is involved in cellular pH homeostasis, providing proton motive force necessary for transport processes, trafficking of proteins and, thereby, cell wall synthesis. The data points to regulation taking place on multiple levels: (a) a phosphorylation-dependent regulation by 14-3-3 proteins and by kinases such as WNK8 and NDPK1a, (b) an energy-dependent regulation via HXK1 and the glucose receptor RGS1 and (c) a Ca2+-dependent regulation by SOS2 and IDQ6. The known importance of V-ATPase for cell wall synthesis is supported by its interactions with several proteins involved in cell wall synthesis. The resulting network was further analyzed for (experimental) biases and was found to be enriched in nuclear, cytosolic and plasma membrane proteins but depleted in extracellular and mitochondrial proteins, in comparison to the entity of protein-coding genes. Among the processes and functions, proteins involved in transcription were highly abundant in the network. Subnetworks were extracted for organelles, processes and protein families. The degree of representation of organelles and processes reveals limitations and advantages in the current knowledge of protein–protein interactions, which have been mainly caused by a high number of database entries being contributed by only a few publications with highly specific motivations and methodologies that favor, for instance, interactions in the cytosol and the nucleus.

Deep sequencing of suppression subtractive library identifies differentially expressed transcripts of Saccharum spontaneum exposed to salinity stress

Saccharum spontaneum, a wild relative of sugarcane, is highly tolerant to drought and salinity. The exploitation of germplasm resources for salinity tolerance is a major thrust area in India. In this study, we utilized suppression subtractive hybridization (SSH) followed by sequencing for the identification of upregulated transcripts during salinity stress in S. spontaneum clones coming from different geographical regions of India. Our sequencing of the SSH library revealed that 95% of the transformants contained inserts of size 200-1500 bp. We have identified 314 differentially expressed transcripts in the salinity-treated samples after subtraction, which were subsequently validated by quantitative real-time polymerase chain reaction. Functional annotation and pathway analysis revealed that the upregulated transcripts were a result of protein modifications, stress, and hormone signaling along with cell wall development and lignification. The prominently upregulated transcripts included UDP glucose dehydrogenase, cellulose synthase, ribulose, cellulose synthase COBRA, leucine-rich protein, NAC domain protein, pectin esterase, ABA-responsive element binding factor 1, and heat stress protein. Our results is a step forward the understanding of the molecular response of S. spontaneum under salinity stress, which will lead to the identification of genes and transcription factors as novel targets for salinity tolerance in sugarcane.

Autophagy during drought: function, regulation, and potential application

Drought is a major challenge for agricultural production since it causes substantial yield reduction and economic loss. Autophagy is a subcellular degradation and recycling pathway that functions in plant development and responses to many stresses, including drought. In this review, we summarize the current understanding of the function of autophagy and how autophagy is upregulated during drought stress. Autophagy helps plants to survive drought stress, and the mechanistic basis for this is beginning to be elucidated. Autophagy can selectively degrade aquaporins to adjust water permeability, and also degrades excess heme and damaged proteins to reduce their toxicity. In addition, autophagy can degrade regulators or components of hormone signaling pathways to promote stress responses. During drought recovery, autophagy degrades drought-induced proteins to reset the cell status. Autophagy is activated by multiple mechanisms during drought stress. Several transcription factors are induced by drought to upregulate autophagy-related gene expression, and autophagy is also regulated post-translationally through protein modification and stability. Based on these observations, manipulation of autophagy activity may be a promising approach for conferring drought tolerance in plants.

Microscopic Imaging of Endosomal Trafficking of ABA Receptors

The abscisic acid (ABA) is a key hormone for stress tolerance. The balance between growth/development and stress responses is crucial for the optimal course of plant life meaning that plants need to control the timing and extent of ABA pathway activation. In this regard, protein turnover regulation by means of both the ubiquitin-proteasome system (UPS) and non-26S proteasome endomembrane trafficking pathways, plays a critical role in the regulation of ABA signaling activation and deactivation. Over the last few years, the ubiquitination of ABA receptors PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS (RCAR) at the plasma membrane by the RING between RING fingers (RBR)-type E3 ligase RING FINGER OF SEED LONGEVITY1 (RSL1) triggering their internalization through the clathrin-mediated endocytosis (CME) pathway, followed by their endosomal trafficking and delivery to the vacuole for degradation, was reported. For this process, the direct role of some components of the endosomal sorting complex required for transport (ESCRT) machinery, that is, FYVE DOMAIN-CONTAINING PROTEIN 1 (FYVE1)/FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1 (FREE1) and VACUOLAR PROTEIN SORTING23A (VPS23A) members of ESCRT-I complex, and ALG-2 INTERACTING PROTEIN-X (ALIX) associated protein of ESCRT-III, was reported. In this chapter, we will detail two methods for imaging endosomal trafficking of ABA receptor proteins by confocal microscopy: (a) colocalization of GFP-PYL4 (also known as RCAR10) and CLATHRIN LIGHT CHAIN 2 (CLC2)-mOrange in clathrin-coated vesicles in Nicotiana benthamiana leaf cells and (b) localization of GFP-PYL4 into Wortmannin (WM)-enlarged late endosomes in Arabidopsis thaliana root cells.

Comprehensive Effects of Flowering Locus T-Mediated Stem Growth in Tobacco

In flowering plants, Flowering locus T (FT) encodes a major florigen. It is a key flowering hormone in controlling flowering time and has a wide range of effects on plant development. Although the mechanism by which FT promotes flowering is currently clearly understood, comprehensive effects of the FT gene on plant growth have not been evaluated. Therefore, the effects of FT on vegetative growth need to be explored for a complete understanding of the molecular functions of the FT gene. In this study, the Jatropha curcas L. FT gene was overexpressed in tobacco (JcFT^OE) in order to discover multiple aspects and related mechanisms of how the FT gene affects plant development. In JcFT^OE plants, root, stem, and leaf development was strongly affected. Stem tissues were selected for further transcriptome analysis. In JcFT^OE plants, stem growth was affected because of changes in the nucleus, cytoplasm, and cell wall. In the nucleus of JcFT^OE plants, the primary effect was to weaken all aspects of DNA replication, which ultimately affected the cell cycle and cell division. The number of stem cells decreased significantly in JcFT^OE plants, which decreased the thickness and height of tobacco stems. In the cell wall of JcFT^OE plants, hemicellulose and cellulose contents increased, with the increase in hemicellulose associated with up-regulation of xylan synthase-related genes expression. In the cytoplasm of JcFT^OE plants, the primary effects were on biogenesis of ribonucleoprotein complexes, photosynthesis, carbohydrate biosynthesis, and the cytoskeleton. In addition, in the cytoplasm of JcFT^OE plants, there were changes in certain factors of the core oscillator, expression of many light-harvesting chlorophyll a/b binding proteins was down-regulated, and expression of fructose 1,6-bisphosphatase genes was up-regulated to increase starch content in tobacco stems. Changes in the xylem and phloem of JcFT^OE plants were also identified, and in particular, xylem development was affected by significant increases in expression of irregular xylem genes.

OsPSKR15, a phytosulfokine receptor from rice enhances abscisic acid response and drought stress tolerance

Abscisic acid (ABA) is a major phytohormone that acts as stimuli and plays an important role in plant growth, development, and environmental stress responses. Membrane-localized receptor-like kinases (RLKs) help to detect extracellular stimuli and activate downstream signaling responses to modulate a variety of biological processes. Phytosulfokine receptor (PSKR), a Leu-rich repeat (LRR)-RLK, has been characterized for its role in growth, development and biotic stress. Here, we observed that OsPSKR15, a rice PSKR, was upregulated by ABA in Oryza sativa. We demonstrated OsPSKR15 is a positive regulator in plant response to ABA. Ectopic expression of OsPSKR15 in Arabidopsis thaliana increased the sensitivity to ABA during germination, growth and stomatal closure. Consistently, the expression of ABA-inducible genes was significantly upregulated in these plants. OsPSKR15 also regulated reactive oxygen species (ROS)-mediated ABA signaling in guard cells, thereby governing stomatal closure. Furthermore, the constitutive expression of OsPSKR15 enhanced drought tolerance by reducing the transpirational water loss in Arabidopsis. We also reported that OsPSKR15 directly interacts with AtPYL9 and its orthologue OsPYL11 of rice through its kinase domain in the plasma membrane and nucleus. Altogether, these results reveal an important role of OsPSKR15 in plant response toward abiotic stress in an ABA-dependent manner.

Core Components of Abscisic Acid Signaling and Their Post-translational Modification

Abscisic acid (ABA) is a major phytohormone that regulates plant growth, development, and abiotic/biotic stress responses. Under stress, ABA is synthesized in various plant organs, and it plays roles in diverse adaptive processes, including seed dormancy, growth inhibition, and leaf senescence, by modulating stomatal closure and gene expression. ABA receptor, clade A protein phosphatase 2C (PP2C), and SNF1-related protein kinase 2 (SnRK2) proteins have been identified as core components of ABA signaling, which is initiated via perception of ABA with receptor and subsequent activation or inactivation by phosphorylation/dephosphorylation. The findings of several recent studies have established that the post-translational modification of these components, including phosphorylation and ubiquitination/deubiquitination, play important roles in regulating their activity and stability. In this review, we discuss the functions of the core components of ABA signaling and the regulation of their activities via post-translational modification under normal and stress conditions.

Genome-Wide Identification and Characterization of DnaJ Gene Family in Grape (Vitis vinifera L.)

Grape production in southern China suffers great loss due to various environmental stresses. To understand the mechanism of how the grape plants respond to these stresses is an active area of research in developing cultivation techniques. Plant stress resistance is known to rely on special proteins. Amongst them, DnaJ protein (HSP40) serves as co-chaperones of HSP70, playing crucial roles in various stress response. However, the DnaJ proteins encoded by the DnaJ gene family in Vitis vinifera L. have not been fully described yet. In this study, we identified 78 VvDnaJs in the grape genome that can be classified into three groups—namely, DJA, DJB, and DJC. To reveal the evolutionary and stress response mechanisms for the VvDnaJ gene family, their evolutionary and expression patterns were analyzed using the bioinformatic approach and qRT-PCR. We found that the members in the same group exhibited a similar gene structure and protein domain organization. Gene duplication analysis demonstrated that segmental and tandem duplication may not be the dominant pathway of gene expansion in the VvDnaJ gene family. Codon usage pattern analysis showed that the codon usage pattern of VvDnaJs differs obviously from the monocotyledon counterparts. Tissue-specific analysis revealed that 12 VvDnaJs present a distinct expression profile, implying their distinct roles in various tissues. Cis-acting element analysis showed that almost all VvDnaJs contained the elements responsive to either hormones or stresses. Therefore, the expression levels of VvDnaJs subjected to exogenous hormone applications and stress treatments were determined, and we found that VvDnaJs were sensitive to hormone treatments and shade, salt, and heat stresses, especially VIT_00s0324g00040. The findings of this study could provide comprehensive information for the further investigation on the genetics and protein functions of the DnaJ gene family in grape.

Plant Proteoforms Under Environmental Stress: Functional Proteins Arising From a Single Gene

Proteins are directly involved in plant phenotypic response to ever changing environmental conditions. The ability to produce multiple mature functional proteins, i.e., proteoforms, from a single gene sequence represents an efficient tool ensuring the diversification of protein biological functions underlying the diversity of plant phenotypic responses to environmental stresses. Basically, two major kinds of proteoforms can be distinguished: protein isoforms, i.e., alterations at protein sequence level arising from posttranscriptional modifications of a single pre-mRNA by alternative splicing or editing, and protein posttranslational modifications (PTMs), i.e., enzymatically catalyzed or spontaneous modifications of certain amino acid residues resulting in altered biological functions (or loss of biological functions, such as in non-functional proteins that raised as a product of spontaneous protein modification by reactive molecular species, RMS). Modulation of protein final sequences resulting in different protein isoforms as well as modulation of chemical properties of key amino acid residues by different PTMs (such as phosphorylation, N- and O-glycosylation, methylation, acylation, S-glutathionylation, ubiquitinylation, sumoylation, and modifications by RMS), thus, represents an efficient means to ensure the flexible modulation of protein biological functions in response to ever changing environmental conditions. The aim of this review is to provide a basic overview of the structural and functional diversity of proteoforms derived from a single gene in the context of plant evolutional adaptations underlying plant responses to the variability of environmental stresses, i.e., adverse cues mobilizing plant adaptive mechanisms to diminish their harmful effects.

Loss-of-function of ARABIDOPSIS F-BOX PROTEIN HYPERSENSITIVE TO ABA 1 enhances drought tolerance and delays germination

ABA is a phytohormone involved in diverse plant events such as seed germination and drought response. An F-box protein functions as a substrate receptor of the SCF complex and is responsible for ubiquitination of target proteins, triggering their subsequent degradation mediated by ubiquitin proteasome system. Here, we have isolated a gene named ARABIDOPSIS F-BOX PROTEIN HYPERSENSITIVE TO ABA 1 (AFA1) that was upregulated by ABA. AFA1 interacted with adaptor proteins of the SCF complex, implying its role as a substrate receptor of the complex. Its loss of function mutants, afa1 seedlings, exhibited ABA-hypersensitivity, including delayed germination in the presence of ABA. Moreover, loss of AFA1 led to increased drought tolerance in adult plants. Microarray data with ABA treatments indicated that 129 and 219 genes were upregulated or downregulated, respectively, by more than three times in afa1 relative to the wild type. Among the upregulated genes in afa1, the expression of 28.7% was induced by more than three times in the presence of ABA, while only 9.3% was repressed to the same extent. These data indicate that AFA1 is involved in the downregulation of many ABA-inducible genes, in accordance with the ABA-hypersensitive phenotype of afa1. Epistasis analysis showed that AFA1 could play a role upstream of ABI4 and ABI5 in the ABA signaling for germination inhibition. Collectively, our findings suggest that AFA1 is a novel F-box protein that negatively regulates ABA signaling.

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.

OsANN4 modulates ROS production and mediates Ca2+ influx in response to ABA

BACKGROUND

Plant annexins are calcium- and lipid-binding proteins that have multiple functions, and a significant amount of research on plant annexins has been reported in recent years. However, the functions of annexins in diverse biological processes in rice are largely unclear.

RESULTS

Herein, we report that OsANN4, a calcium-binding rice annexin protein, was induced by abscisic acid (ABA). Under ABA treatment, the plants in which OsANN4 was knocked down by RNA interference showed some visible phenotypic changes compared to the wild type, such as a lower rooting rate and shorter shoot and root lengths. Moreover, the superoxide dismutase (SOD) and catalase (CAT) activities of the RNAi lines were significantly lower and further resulted in higher accumulation of O₂^.- and H₂O₂ than those of the wild-type. A Non-invasive Micro-test Technology (NMT) assay showed that ABA-induced net Ca²⁺ influx was inhibited in OsANN4 knockdown plants. Interestingly, the phenotypic differences caused by ABA were eliminated in the presence of LaCl₃ (Ca²⁺ channel inhibitor). Apart from this, we demonstrated that OsCDPK24 interacted with and phosphorylated OsANN4. When the phosphorylated serine residue of OsANN4 was substituted by alanine, the interaction between OsANN4 and OsCDPK24 was still observed, however, both the conformation of OsANN4 and its binding activity with Ca²⁺ might be changed.

CONCLUSIONS

OsANN4 plays a crucial role in the ABA response, partially by modulating ROS production, mediating Ca²⁺ influx or interacting with OsCDPK24.

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.

Pepper ubiquitin-specific protease, CaUBP12, positively modulates dehydration resistance by enhancing CaSnRK2.6 stability

Abscisic acid (ABA) is a plant hormone that activates adaptive mechanisms to environmental stress conditions. Plant adaptive mechanisms are complex and highly modulated processes induced by stress-responsive proteins; however, the precise mechanisms by which these processes function under adverse conditions remain unclear. Here, we isolated CaUBP12 (Capsicum annuum ubiquitin-specific protease 12) from pepper (C. annuum) leaves. We show that CaUBP12 expression is significantly induced after exposure to abiotic stress treatments. We conducted loss-of-function and gain-of-function genetic studies to elucidate the biological functions of CaUBP12 in response to ABA and dehydration stress. CaUBP12-silenced pepper plants and CaUBP12-overexpressing Arabidopsis plants displayed dehydration-sensitive and dehydration-tolerant phenotypes, respectively; these phenotypes were characterized by regulation of transpirational water loss and stomatal aperture. Under dehydration stress conditions, CaUBP12-silenced pepper plants and CaUBP12-overexpressing Arabidopsis plants exhibited lower and higher expression levels of stress-related genes, respectively, than the control plants. We isolated a CaUBP12 interaction protein, CaSnRK2.6, which is a homolog of Arabidopsis OST1; degradation of this protein was partially inhibited by CaUBP12. Similar to CaUBP12-silenced pepper plants and CaUBP12-overexpressing Arabidopsis plants, CaSnRK2.6-silenced pepper plants and CaSnRK2.6-overexpressing Arabidopsis displayed dehydration-sensitive and dehydration-tolerant phenotypes, respectively. Our findings suggest that CaUBP12 positively modulates the dehydration stress response by suppressing CaSnRK2.6 protein degradation.

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.

Arabidopsis OSMOTIN 34 Functions in the ABA Signaling Pathway and Is Regulated by Proteolysis

Plants have evolutionarily established resistance responses to a variety of abiotic stress conditions, in which ABA mediates the integrated regulation of these stress responses. Numerous proteins function at the transcription level or at the protein level when contributing to controls of the ABA signaling process. Although osmotin is identified as a salt-inducible protein, its function in the abiotic stress response is yet to be elucidated. To examine the role of Arabidopsis OSMOTIN 34 (OSM34) in the ABA signaling pathway, a deletion mutant osm34 generated by a CRISPR/Cas9 system and the double mutant osm34 osml (osmotin 34-like) were analyzed for various ABA responses. Both osm34 and osm34 osml showed reduced levels of ABA responses in seeds and leaves. Moreover, proline level and expression of the proline biosynthesis gene P5CS1 was significantly reduced in osm34 osml. Interestingly, OSM34 binds to SKP2A, an F-Box protein whose transcription is induced by ABA. The protein stability of OSM34 was determined to be under the control of the 26S proteasome. In conclusion, our data suggest that OSM34 functions as a positive regulator in the generation of ABA responses and is under post-translational control.

Cloning and expression analyses of a Pyrabactin Resistance 1 (PYR1) gene from Magnolia sieboldii K. Koch

Magnolia sieboldii K. Koch is endemic to China and has high medicinal and ornamental values. However, its seed exhibits morphophysiological dormancy, and the molecular mechanisms of which are not clearly understood. To reveal the regulation mechanism of the ABA signal in seed dormancy, the M. sieboldii ABA receptor Pyrabactin Resistance 1 (PYR1) gene was cloned and analyzed. Analysis of the MsPYR1 sequence analysis showed that the full-length cDNA contained a complete open reading frame of 987 bp and encoded a predicted protein of 204 amino acid residues. The protein had a relative molecular weight of 22.661 kDa and theoretical isoelectric point of 5.01. The transcript levels of MsPYR1 were immediately upregulated at 16 DAI and then decreased at 40 DAI. The highest transcript level of MsPYR1 was found in the dry seeds, indicating that the MsPYR1 gene may play an important role in the regulation of dormancy. The MsPYR1 gene cDNA was successfully expressed in E. coli Rosetta (DE3), and the protein bands were consistent with the prediction. The Anti-MsPYR1antibody could detect the expression of MsPYR1 in M. sieboldii. The results provided a foundation for further study of the function of the MsPYR1 gene.ABBREVIATIONSABA: Abscisic acid; MPD: morphophysiological; PYR1: Pyrabactin Resistance1; PYL: Pyr1-Like; RCAR: Regulatory Components of Aba Receptors; PP2C: protein phosphatases 2C; SnRK2: sucrose non-fermenting1-related protein kinase2; DAI: day after imbibition; NCBI: National Center for Biotechnology Information; BCA: Bicinchoninic acid; CDD: Conserved Domains.

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.

Small kernel 501 (smk501) encodes the RUBylation activating enzyme E1 subunit ECR1 (E1 C-TERMINAL RELATED 1) and is essential for multiple aspects of cellular events during kernel development in maize

RUBylation plays essential roles in plant growth and development through regulating Cullin-RING ubiquitin E3 ligase (CRL) activities and the CRL-mediated protein degradations. However, the function of RUBylation in regulating kernel development remains unclear. Through genetic and molecular analyses of a small kernel 501 (smk501) mutant in maize (Zea mays), we cloned the smk501 gene, revealed its molecular function, and defined its roles in RUBylation pathway and seed development. Smk501 encodes a RUBylation activating enzyme E1 subunit ZmECR1 (E1 C-TERMINAL RELATED 1) protein. Destruction in RUBylation by smk501 mutation resulted in less embryo and endosperm cell number and smaller kernel size. The transcriptome and proteome profiling, hormone evaluation and cell proliferation observation revealed that disturbing ZmECR1 expression mainly affects pathways on hormone signal transduction, cell cycle progression and starch accumulation during kernel development. In addition, mutant in zmaxr1 (Auxin resistant 1), another RUB E1 subunit, also showed similar defects in kernel development. Double mutation of zmecr1 and zmaxr1 lead to empty pericarp kernel phenotype. RUBylation is a novel regulatory pathway affecting maize kernel development, majorly through its functions in modifying multiple cellular progresses.

Pepper E3 ligase CaAIRE1 promotes ABA sensitivity and drought tolerance by degradation of protein phosphatase CaAITP1

Plants have developed defense mechanisms to survive in extreme environmental conditions. Abscisic acid (ABA) is a key phytohormone associated with plant adaptation to environmental stress. In this study, we isolated and functionally characterized the pepper RING-type E3 ligase CaAIRE1 (Capsicum annuum ABA Induced RING-type E3 ligase 1) containing the C3HC4-type RING domain. CaAIRE1 was induced by ABA and drought, and CaAIRE1 had E3 ligase activity. CaAIRE1-silenced pepper and CaAIRE1-overexpressing Arabidopsis presented drought-sensitive and drought-tolerant phenotypes, respectively, which were accompanied by altered transpiration water loss and ABA sensitivity. Moreover, we found that CaAIRE1 interacts with and ubiquitinates the pepper type 2C protein phosphatase, CaAITP1 (Capsicum annuum CaAIRE1 Interacting Target Phosphatase 1). A cell-free degradation assay with CaAIRE1-silenced peppers and CaAIRE1-overexpressing Arabidopsis plants revealed that the CaAITP1 protein level was negatively modulated by the expression level of CaAIRE1. In contrast to CaAIRE1, CaAITP1-silenced pepper showed ABA-sensitivity phenotypes. CaAITP1-overexpressing Arabidopsis plants were the most insensitive phenotypes to ABA compared with the wild type and other pepper PP2C-overexpressing plants. Taken together, our data indicate that CaAITP1 plays a major role as a negative modulator in ABA signaling, and CaAIRE1 regulates the ABA signaling and drought response through modulation of CaAITP1 stability.

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.

A ras-related small GTP-binding protein, RabE1c, regulates stomatal movements and drought stress responses by mediating the interaction with ABA receptors

Drought represents a leading constraint over crop productivity worldwide. The plant response to this stress is centered on the behavior of the cell membrane, where the transduction of abscisic acid (ABA) signaling occurs. Here, the Ras-related small GTP-binding protein RabE1c has been shown able to bind to an ABA receptor in the Arabidopsis thaliana plasma membrane, thereby positively regulating ABA signaling. RabE1c is highly induced by drought stress and expressed abundantly in guard cells. In the loss-of-function rabe1c mutant, both stomatal closure and the whole plant drought stress response showed a reduced sensitivity to ABA treatment, demonstrating that RabE1c is involved in the control over transpirative water loss through the stomata. Impairment of RabE1c's function suppressed the accumulation of the ABA receptor PYL4. The over-expression of RabE1c in A. thaliana enhanced the plants' ability to tolerate drought, and a similar phenotypic effect was achieved by constitutively expressing the gene in Chinese cabbage (Brassica rapassp. pekinensis). The leading conclusion was that RabE1c promotes the degradation of PYL4, suggesting a possible genetic strategy to engineer crop plants to better withstand drought stress.

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.