Arabidopsis RZFP34/CHYR1, a Ubiquitin E3 Ligase, Regulates Stomatal Movement and Drought Tolerance via SnRK2.6-Mediated Phosphorylation

Soybean RING-type E3 ligase GmCHYR16 ubiquitinates the GmERF71 transcription factor for degradation to negatively regulate bicarbonate stress tolerance

Plant AP2/ERF (APETALA2/ethylene response factor) transcription factors are key regulators of environmental stress tolerance. We previously characterized that the wild soybean ERF71 transcription factor conferred bicarbonate stress tolerance; however, the underlying mechanism still remains elusive. Here, multiple approaches were used to identify the E3 ubiquitin ligase GmCHYR16 as an interactor of GmERF71. Ubiquitination and protein degradation of GmERF71 mediated by GmCHYR16 were then analyzed. Overexpression transgenic lines were generated to evaluate the function of GmCHYR16 and GmERF71 in bicarbonate stress response. GmCHYR16 interacts with GmERF71. GmERF71 proteins undergo ubiquitination and 26S proteasome-mediated degradation, and GmCHYR16 mediates the ubiquitination of GmERF71 for degradation. The GmCHYR16-mediated ubiquitination and proteasome-dependent degradation of GmERF71 are reduced under bicarbonate stress. GmCHYR16 expression in transgenic Arabidopsis, soybean hairy roots, and stable transgenic soybean reduces bicarbonate stress tolerance. GmERF71 degradation is decreased in the protein extracts of atchyr1/7 mutants, and atchyr1/7 mutants display higher bicarbonate tolerance. Overexpression of GmERF71 in transgenic soybean obviously increases bicarbonate tolerance, and GmCHYR16 reduces the bicarbonate tolerance of transgenic hairy root composite soybean plants by repressing GmERF71. Our results demonstrate that GmCHYR16 directly ubiquitinates GmERF71 for degradation and negatively regulates bicarbonate stress tolerance.

AREB/ABF/ABI5 transcription factors in plant defense: regulatory cascades and functional diversity

Basic leucine zipper transcription factors (TFs), also known as ABRE-BINDING PROTEINs/ABRE BINDING FACTORs (AREBs/ABFs), and ABA INSENSITIVE 5 (ABI5), show a great potential for the regulation of gene expressions in different crops under unfavorable conditions. These factors are involved in phytohormone signaling pathways, developmental metabolism, and growth regulation under environmental stresses. ABI5 functions alongside ABREs to regulate gene expression, with their promoter regions composed of the receptors PYR/PYL/RCAR, kinases (sucrose non-fermenting-1-related protein kinase 2) and phosphatases (PROTEIN PHOSPHATASE 2 C). These TFs participate in signaling pathways that regulate key genes and control numerous morphological, physiological, biochemical, and molecular processes under stressful environments. In this review, we studied ABFs/AREBs/ABI5s TFs, the phytohormone signaling pathways and their crosstalk, which play critical roles in regulating responses to abiotic stresses. The key TFs discussed in this work regulate various metabolic pathways and are promising candidates for the development of stress-resilient crops via CRISPR/CRISPR-associated protein technology to address threats to food security and sustainability in agriculture.

Structural Dynamics, Evolutionary Significance, and Functions of Really Interesting New Gene Proteins in Ubiquitination and Plant Stress: A Review

Abiotic stress causes major crop losses worldwide. Plants have evolved complex intricate signaling network involving transcriptional regulators and posttranslational modifications (PTMs). Ubiquitination-a key PTM-regulates protein degradation through the ubiquitin-proteasome system (UPS). The UPS plays a pivotal role in detecting and modulating plant responses to environmental fluctuations. The E3 ligase family in plants is extensive, offering high substrate specificity and playing a vital role in signaling and protein turnover. Really Interesting New Gene (RING) proteins primarily function as E3 ubiquitin ligases, their functional diversity facilitates the transfer of ubiquitin molecules to specific target proteins. Plants possess abscisic acid (ABA)-dependent and ABA-independent stress-signaling pathways. RING-type E3 ligases regulate ABA signaling either negatively or positively in response to stress by regulating protein degradation, modulating transcription factors, ABA biosynthesis, and degradation. This dynamic interaction between ABA and E3 ligase proteins helps plants to adapt to environmental stress. Negative regulators, such as AIP2 and OsDSG1, target ABI3 for degradation. Keep on going (KEG) ubiquitinates ABI5, ABF1, and ABF3, though KEG itself is subject to feedback regulation by ABA levels, leading to its degradation. Positive regulators include SDIR1, OsSDIR1, AIRP1, RHA2b/RHA2a, and XERICO, along with its maize orthologs ZmXerico1 and ZmXerico2. Additionally, SINAT5 and BOI regulate auxin and gibberellin signaling, integrating hormonal responses to stress. The functional diversity of RING-type E3 ligases offers promising targets for genetic engineering to enhance crop resilience under adverse environmental conditions. Understanding these molecular mechanisms could lead to the development of climate-resilient crops, crucial for sustaining global food security.

SnRK2s: Kinases or Substrates?

Throughout their life cycle, plants persistent through environmental adversities that activate sophisticated stress-signaling networks, with protein kinases serving as pivotal regulators of these responses. The sucrose non-fermenting-1-related protein kinase 2 (SnRK2), a plant-specific serine/threonine kinase, orchestrates stress adaptation by phosphorylating downstream targets to modulate gene expression and physiological adjustments. While SnRK2 substrates have been extensively identified, the existing literature lacks a systematic classification of these components and their functional implications. This review synthesizes recent advances in characterizing SnRK2-phosphorylated substrates in Arabidopsis thaliana, providing a mechanistic framework for their roles in stress signaling and developmental regulation. Furthermore, we explore the understudied paradigm of SnRK2 undergoing multilayered post-translational modifications (PTMs), including phosphorylation, ubiquitination, SUMOylation, S-nitrosylation, sulfation (S-sulfination and tyrosine sulfation), and N-glycosylation. These PTMs collectively fine-tune SnRK2 stability, activity, and subcellular dynamics, revealing an intricate feedback system that balances kinase activation and attenuation. By integrating substrate networks with regulatory modifications, this work highlights SnRK2's dual role as both a phosphorylation executor and a PTM-regulated scaffold, offering new perspectives for engineering stress-resilient crops through targeted manipulation of SnRK2 signaling modules.

Genome-wide analysis of CHYR gene family and BnA03.CHYR.1 functional verification under salt stress in Brassica napus L

Brassica napus, an allotetraploid used as an oilseed crop, vegetable, or feed crop, possesses significant economic and medicinal value. Although the CHYR gene family has been functionally characterised in various aspects of plant growth, development, and stress responses, its systematic investigation in B. napus is lacking. In contrast to the seven CHYR genes (AtCHYR1-AtCHYR7) identified in Arabidopsis thaliana, nine CHYR orthologues were detected in B. rapa and B. oleracea, while 24 were found in B. napus. This discrepancy is consistent with the established triplication events that occurred during the Brassicaceae family evolution. Phylogenetic analysis indicated that the 24 CHYRs identified in B. napus could be categorised into three distinct groups. Among these, 24 BnCHYRs contained conserved domains, including the CHY-zinc finger, C3H2C3-type RING finger and zinc ribbon domains. Group III members featured an additional one to three hemerythrin domains in their N-terminal regions. Each BnCHYR group shared similar patterns in the distribution of conserved domains. Our results revealed that the selected eight BnCHYRs were up-regulated following heat treatment, exhibiting varying expression patterns in response to salt, cold, and drought stress during the seedling stage. Expression analysis revealed that several BnCHYRs were significantly induced by one or more abiotic stressors. BnA03.CHYR.1 was significantly induced by salt and heat stress and repressed by polyethylene glycol treatment. BnA03.CHYR.1 was localised in the nucleus and cytoplasm, and its overexpression in A. thaliana enhanced tolerance to salt stress. Our results provide a comprehensive analysis of the CHYR family in B. napus, elucidating the biological role of BnA03.CHYR.1 in adaptive responses of plants to salt stress.

An LRR-RLK protein modulates drought- and salt-stress responses in maize

Maize (Zea mays), which is a vital source of food, feed, and energy feedstock globally, has significant potential for higher yields. However, environmental stress conditions, including drought and salt stress, severely restrict maize plant growth and development, leading to great yield losses. Leucine-rich repeat receptor-like kinases (LRR-RLKs) function in biotic and abiotic stress responses in the model plant Arabidopsis (Arabidopsis thaliana), but their roles in abiotic stress responses in maize are not entirely understood. In this study, we determine that the LRR-RLK ZmMIK2, a homolog of the Arabidopsis LRR-RK MALE DISCOVERER 1 (MDIS1)-INTERACTING RECEPTOR LIKE KINASE 2 (MIK2), functions in resistance to both drought and salt stress in maize. Zmmik2 plants exhibit enhanced resistance to both stresses, whereas overexpressing ZmMIK2 confers the opposite phenotypes. Furthermore, we identify C2-DOMAIN-CONTAINING PROTEIN 1 (ZmC2DP1), which interacts with the intracellular region of ZmMIK2. Notably, that region of ZmMIK2 mediates the phosphorylation of ZmC2DP1, likely by increasing its stability. Both ZmMIK2 and ZmC2DP1 are mainly expressed in roots. As with ZmMIK2, knockout of ZmC2DP1 enhances resistance to both drought and salt stress. We conclude that ZmMIK2-ZmC2DP1 acts as a negative regulatory module in maize drought- and salt-stress responses.

Regulation of Stomatal Responses to Pathogen and Drought Stress by the F-Box Protein AtSKIP5

E3 ubiquitin ligases are major components of the ubiquitination cascade and contribute to the stomatal responses to pathogen and drought stress in plants. The F-box SKP1-Interacting Partners (AtSKIPs) proteins are members of the SCF E3 ubiquitin ligase complexes; however, whether they have any involvement in stomatal movement remains unclear. Here, based on tissue expression profiling, we found that the AtSKIP5 protein was highly expressed in guard cells. Mutation of AtSKIP5 rendered plants more susceptible to Pseudomonas syringae pv. tomato (Pst) DC3000 and resulted in a significant impairment in stomatal closure after flg22 and Pst DC3000 treatment. Consistently, lines overexpressing AtSKIP5 were more resistant to Pst DC3000 infection and exhibited more rapid stomatal closure than did other lines. However, the AtSKIP5-overexpressing lines and Col-0 line were similarly resistant to Pst- (coronatine-deficient mutant) infection and did not exhibit stomatal reopening when exposed to Pst DC3000, a Pst- strain, or a Pst- strain accompanied by coronatine (COR) treatment. These results suggest that AtSKIP5-mediated resistance to Pst DC3000 is by controlling stomatal immunity via positive regulation of flg22-triggered stomatal closure and suppression of COR-mediated stomatal reopening. Furthermore, apoplastic immunity was compromised in the skip5 mutants, as evidenced by lower MAPK phosphorylation levels, less reactive oxygen species (ROS) production, and callose deposition induced by flg22, shifting the response in the pathogenic direction. In addition, the skip5 mutants evidenced an impairment in stomatal closure induced by abscisic acid (ABA), and a lower survival rate and greater water loss under drought stress, suggesting that AtSKIP5 serves as a positive regulator of drought tolerance via ABA-induced stomatal closure. Our results provide new insights into the importance of the stomatal responses to pathogen and drought stresses that are modulated by AtSKIP5 in Arabidopsis.

Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice (Zizania palustris L.)

Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic, annual grass with significant ecological, cultural, and economic importance to the Great Lakes region of North America. In this study, we assembled and genotyped a diverse collection of 839 NWR individuals using genotyping-by-sequencing (GBS) and obtained 5955 single-nucleotide polymorphisms (SNPs). This collection consisted of samples from 12 wild NWR populations collected across Minnesota and Western Wisconsin, some of which were collected over two time points; a representative collection of cultivated NWR varieties and breeding populations; and a Zizania aquatica outgroup. Using these data, we characterized the genetic diversity, relatedness, and population structure of this broad collection of NWR genotypes. We found that wild populations of NWR clustered primarily by their geographical location, with some clustering patterns likely influenced by historical ecosystem management. Cultivated populations were genetically distinct from wild populations, suggesting limited gene flow between the semi-domesticated crop and its wild counterparts. The first genome-wide scans of putative selection events in cultivated NWR suggest that the crop is undergoing heavy selection pressure for traits conducive to irrigated paddy conditions. Overall, this study presents a large set of SNP markers for use in NWR genetic studies and provides new insights into the gene flow, history, and complexity of wild and cultivated populations of NWR.

MYB30-INTERACTING E3 LIGASE 1 regulates LONELY GUY 5-mediated cytokinin metabolism to promote drought tolerance in cotton

Ubiquitination plays important roles in modulating the abiotic stress tolerance of plants. Drought seriously restricts agricultural production, but how ubiquitination participates in regulating drought tolerance remains largely unknown. Here, we identified a drought-inducible gene, MYB30-INTERACTING E3 LIGASE 1 (GhMIEL1), which encodes a RING E3 ubiquitin ligase in cotton (Gossypium hirsutum). GhMIEL1 was strongly induced by polyethylene glycol (PEG-6000) and the phytohormone abscisic acid. Overexpression and knockdown of GhMIEL1 in cotton substantially enhanced and reduced drought tolerance, respectively. GhMIEL1 interacted with the MYB transcription factor GhMYB66 and could ubiquitinate and degrade it in vitro. GhMYB66 directly bound to the LONELY GUY 5 (GhLOG5) promoter, a gene encoding cytokinin riboside 5'-monophosphate phosphoribohydrolase, to repress its transcription. Overexpression of GhMIEL1 and silencing of GhMYB66 altered the homeostasis of cytokinin of plant roots, increased total root length and number of root tips, and enhanced plant drought tolerance. Conversely, silencing GhLOG5 decreased total root length and number of root tips and reduced plant drought tolerance. Our studies reveal that the GhMIEL1-GhMYB66-GhLOG5 module positively regulates drought tolerance in cotton, which deepens our understanding of plant ubiquitination-mediated drought tolerance and provides insights for improving drought tolerance.

De novo transcriptome assembly and discovery of drought-responsive genes in white spruce (Picea glauca)

Forests face an escalating threat from the increasing frequency of extreme drought events driven by climate change. To address this challenge, it is crucial to understand how widely distributed species of economic or ecological importance may respond to drought stress. In this study, we examined the transcriptome of white spruce (Picea glauca (Moench) Voss) to identify key genes and metabolic pathways involved in the species' response to water stress. We assembled a de novo transcriptome, performed differential gene expression analyses at four time points over 22 days during a controlled drought stress experiment involving 2-year-old plants and three genetically distinct clones, and conducted gene enrichment analyses. The transcriptome assembly and gene expression analysis identified a total of 33,287 transcripts corresponding to 18,934 annotated unique genes, including 4,425 genes that are uniquely responsive to drought. Many transcripts that had predicted functions associated with photosynthesis, cell wall organization, and water transport were down-regulated under drought conditions, while transcripts linked to abscisic acid response and defense response were up-regulated. Our study highlights a previously uncharacterized effect of drought stress on lipid metabolism genes in conifers and significant changes in the expression of several transcription factors, suggesting a regulatory response potentially linked to drought response or acclimation. Our research represents a fundamental step in unraveling the molecular mechanisms underlying short-term drought responses in white spruce seedlings. In addition, it provides a valuable source of new genetic data that could contribute to genetic selection strategies aimed at enhancing the drought resistance and resilience of white spruce to changing climates.

The ubiquitin E3 ligase RZFP1 affects drought tolerance in poplar by mediating the degradation of the protein phosphatase PP2C-9

Abscisic acid (ABA) signaling has been implicated in plant responses to water deficit-induced osmotic stress. However, the underlying molecular mechanism remains unelucidated. This study identified the RING-type E3 ubiquitin ligase RING ZINC FINGER PROTEIN1 (PtrRZFP1) in poplar (Populus trichocarpa), a woody model plant. PtrRZFP1 encodes an ubiquitin E3 ligase that participates in protein ubiquitination. PtrRZFP1 mainly functions in the nucleus and endoplasmic reticulum and is activated by drought and ABA. PtrRZFP1-overexpressing transgenic poplars (35S:PtrRZFP1) showed greater tolerance to drought, whereas PtrRZFP1-knockdown lines (KD-PtrRZFP1) showed greater sensitivity to drought. Under treatment with polyethylene glycol and ABA, PtrRZFP1 promoted the production of nitric oxide and hydrogen peroxide in stomatal guard cells, ultimately enhancing stomatal closure and improving drought tolerance. Additionally, PtrRZFP1 physically interacted with the clade A Protein Phosphatase 2C protein PtrPP2C-9, a core regulator of ABA signaling, and mediated its ubiquitination and eventual degradation through the ubiquitination-26S proteasome system, indicating that PtrRZFP1 positively regulates the ABA signaling pathway. Furthermore, the PtrPP2C-9-overexpression line was insensitive to ABA and more sensitive to drought than the wild-type plants, whereas the opposite phenotype was observed in 35S:PtrRZFP1 plants. In general, PtrRZFP1 negatively regulates the stability of PtrPP2C-9 to mediate poplar drought tolerance. The results of this study provide a theoretical framework for the targeted breeding of drought-tolerant traits in perennial woody plants.

Mechanical forces orchestrate the metabolism of the developing oilseed rape embryo

The initial free expansion of the embryo within a seed is at some point inhibited by its contact with the testa, resulting in its formation of folds and borders. Although less obvious, mechanical forces appear to trigger and accelerate seed maturation. However, the mechanistic basis for this effect remains unclear. Manipulation of the mechanical constraints affecting either the in vivo or in vitro growth of oilseed rape embryos was combined with analytical approaches, including magnetic resonance imaging and computer graphic reconstruction, immunolabelling, flow cytometry, transcriptomic, proteomic, lipidomic and metabolomic profiling. Our data implied that, in vivo, the imposition of mechanical restraints impeded the expansion of testa and endosperm, resulting in the embryo's deformation. An acceleration in embryonic development was implied by the cessation of cell proliferation and the stimulation of lipid and protein storage, characteristic of embryo maturation. The underlying molecular signature included elements of cell cycle control, reactive oxygen species metabolism and transcriptional reprogramming, along with allosteric control of glycolytic flux. Constricting the space allowed for the expansion of in vitro grown embryos induced a similar response. The conclusion is that the imposition of mechanical constraints over the growth of the developing oilseed rape embryo provides an important trigger for its maturation.

PagTPS1 and PagTPS10, the trehalose-6-phosphate synthase genes, increase trehalose content and enhance drought tolerance

Trehalose-6-phosphate synthase (TPS) genes play an active role in the trehalose metabolism pathway that regulates the responses of plants to diverse stresses. However, the functional identification, comparison, and conservatism of TPS genes in the responses of woody plants, especially poplars, to drought stress remain unclear. Here, the trehalose content of 84K (Populus alba × P. glandulosa) poplars was down-regulated and PagTPS and PagTPP genes had diverse response patterns under drought stress. Physicochemical properties, expression patterns, and functions of PagTPS1 and PagTPS10, two class I members of TPS gene family, were identified and compared. Transgenic 84K poplars overexpressing PagTPS1 and PagTPS10 had significantly higher trehalose content with approximately 138% and 123%, respectively, and stronger drought tolerance compared to WT. PagTPS1 and PagTPS10 promoted the expression of TPPA genes and drought-responsive genes. Accordingly, poplars inhibiting PagTPS1 and PagTPS10 expression via RNA interference had lower trehalose content and drought tolerance. Simultaneously, overexpressing PagTPS1 and PagTPS10 improved the trehalose content and drought tolerance of Arabidopsis. Overall, we proposed a model of the effects of PagTPS1 and PagTPS10 as conservative regulators on the responses of plants to drought, which would provide new insights into the functional explorations of TPS genes in plants.

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.

A review on ubiquitin ligases: Orchestrators of plant resilience in adversity

Ubiquitin- proteasome system (UPS) is universally present in plants and animals, mediating many cellular processes needed for growth and development. Plants constantly defend themselves against endogenous and exogenous stimuli such as hormonal signaling, biotic stresses such as viruses, fungi, nematodes, and abiotic stresses like drought, heat, and salinity by developing complex regulatory mechanisms. Ubiquitination is a regulatory mechanism involving selective elimination and stabilization of regulatory proteins through the UPS system where E3 ligases play a central role; they can bind to the targets in a substrate-specific manner, followed by poly-ubiquitylation, and subsequent protein degradation by 26 S proteasome. Increasing evidence suggests different types of E3 ligases play important roles in plant development and stress adaptation. Herein, we summarize recent advances in understanding the regulatory roles of different E3 ligases and primarily focus on protein ubiquitination in plant-environment interactions. It also highlights the diversity and complexity of these metabolic pathways that enable plant to survive under challenging conditions. This reader-friendly review provides a comprehensive overview of E3 ligases and their substrates associated with abiotic and biotic stresses that could be utilized for future crop improvement.

The F-Box Protein TaFBA1 Positively Regulates Drought Resistance and Yield Traits in Wheat

Environmental stresses, including drought stress, seriously threaten food security. Previous studies reported that wheat F-box protein, TaFBA1, responds to abiotic stresses in tobacco. Here, we generated transgenic wheat with enhanced (overexpression, OE) or suppressed (RNA interference, RNAi) expression of TaFBA1. The TaFBA1-OE seedlings showed enhanced drought tolerance, as measured by survival rate and fresh weight under severe drought stress, whereas the RNAi plants showed the opposite phenotype. Furthermore, the OE plants had stronger antioxidant capacity compared to WT and RNAi plants and maintained stomatal opening, which resulted in higher water loss under drought stress. However, stronger water absorption capacity in OE roots contributed to higher relative water contents in leaves under drought stress. Moreover, the postponed stomatal closure in OE lines helped to maintain photosynthesis machinery to produce more photoassimilate and ultimately larger seed size. Transcriptomic analyses conducted on WT and OE plants showed that genes involved in antioxidant, fatty acid and lipid metabolism and cellulose synthesis were significantly induced by drought stress in the leaves of OE lines. Together, our studies determined that the F-box protein TaFBA1 modulated drought tolerance and affected yield in wheat and the TaFBA1 gene could provide a desirable target for further breeding of wheat.

Genome-Wide Identification of CHYR Gene Family in Sophora alopecuroides and Functional Analysis of SaCHYR4 in Response to Abiotic Stress

Sophora alopecuroides has important uses in medicine, wind breaking, and sand fixation. The CHY-zinc-finger and RING-finger (CHYR) proteins are crucial for plant growth, development, and environmental adaptation; however, genetic data regarding the CHYR family remain scarce. We aimed to investigate the CHYR gene family in S. alopecuroides and its response to abiotic stress, and identified 18 new SaCHYR genes from S. alopecuroides whole-genome data, categorized into 3 subclasses through a phylogenetic analysis. Gene structure, protein domains, and conserved motifs analyses revealed an exon-intron structure and conserved domain similarities. A chromosome localization analysis showed distribution across 12 chromosomes. A promoter analysis revealed abiotic stress-, light-, and hormone-responsive elements. An RNA-sequencing expression pattern analysis revealed positive responses of SaCHYR genes to salt, alkali, and drought stress. SaCHYR4 overexpression considerably enhanced alkali and drought tolerance in Arabidopsis thaliana. These findings shed light on SaCHYR's function and the resistance mechanisms of S. alopecuroides, presenting new genetic resources for crop resistance breeding.

Combined GWAS and eGWAS reveals the genetic basis underlying drought tolerance in emmer wheat (Triticum turgidum L.)

Drought is one of the major environmental constraints for wheat production world-wide. As the progenitor and genetic reservoir of common wheat, emmer wheat is considered as an invaluable gene pool for breeding drought-tolerant wheat. Combining GWAS and eGWAS analysis of 107 accessions, we identified 86 QTLs, 105 462 eQTLs as well as 68 eQTL hotspots associating with drought tolerance (DT) in emmer wheat. A complex regulatory network composed of 185 upstream regulator and 2432 downstream drought-responsive candidates was developed, of which TtOTS1 was found to play a negative effect in determining DT through affecting root development. This study sheds light on revealing the genetic basis underlying DT, which will provide the indispensable genes and germplasm resources for elite drought tolerance wheat improvement and breeding.

OsMAPK6 phosphorylation and CLG1 ubiquitylation of GW6a non-additively enhance rice grain size through stabilization of the substrate

The chromatin modifier GRAIN WEIGHT 6a (GW6a) enhances rice grain size and yield. However, little is known about its gene network determining grain size. Here, we report that MITOGEN-ACTIVED PROTEIN KINASE 6 (OsMAPK6) and E3 ligase CHANG LI GENG 1 (CLG1) interact with and target GW6a for phosphorylation and ubiquitylation, respectively. Unexpectedly, however, in vitro and in vivo assays reveal that both of the two post-translational modifications stabilize GW6a. Furthermore, we uncover two major GW6a phosphorylation sites (serine142 and threonine186) targeted by OsMAPK6 serving an important role in modulating grain size. In addition, our genetic and molecular results suggest that the OsMAPK6-GW6a and CLG1-GW6a axes are crucial and operate in a non-additive manner to control grain size. Overall, our findings identify a previously unknown mechanism by which phosphorylation and ubiquitylation non-additively stabilize GW6a to enhance grain size, and reveal correlations and interactions of these posttranslational modifications during rice grain development.

H3K27 demethylase SsJMJ4 negatively regulates drought-stress responses in sugarcane

Sugarcane (Saccharum spp.), a leading sugar and energy crop, is seriously impacted by drought stress. However, the molecular mechanisms underlying sugarcane drought resistance, especially the functions of epigenetic regulators, remain elusive. Here, we show that a S. spontaneum KDM4/JHDM3 group JmjC protein, SsJMJ4, negatively regulates drought-stress responses through its H3K27me3 demethylase activity. Ectopic overexpression of SsJMJ4 in Arabidopsis reduced drought resistance possibly by promoting expression of AtWRKY54 and AtWRKY70, encoding two negative regulators of drought stress. SsJMJ4 directly bound to AtWRKY54 and AtWRKY70, and reduced H3K27me3 levels at these loci to ensure their proper transcription under normal conditions. Drought stress down-regulated both transcription and protein abundance of SsJMJ4, which was correlated with the reduced occupancy of SsJMJ4 at AtWRKY54 and AtWRKY70 chromatin, increased H3K27me3 levels at these loci, as well as reduced transcription levels of these genes. In S. spontaneum, drought stress-repressed transcription of SsWRKY122, an ortholog of AtWRKY54 and AtWRKY70, was associated with increased H3K27me3 levels at these loci. Transient overexpression of SsJMJ4 in S. spontaneum protoplasts raised transcription of SsWRKY122, paralleled with reduced H3K27me3 levels at its loci. These results suggest that the SsJMJ4-mediated dynamic deposition of H3K27me3 is required for an appropriate response to drought stress.

OsNAC120 balances plant growth and drought tolerance by integrating GA and ABA signaling in rice

The crosstalk between gibberellin (GA) and abscisic acid (ABA) signaling is crucial for balancing plant growth and adaption to environmental stress. Nevertheless, the molecular mechanism of their mutual antagonism still remains to be fully clarified. In this study, we found that knockout of the rice NAC (NAM, ATAF1/2, CUC2) transcription factor gene OsNAC120 inhibits plant growth but enhances drought tolerance, whereas OsNAC120 overexpression produces the opposite results. Exogenous GA can rescue the semi-dwarf phenotype of osnac120 mutants, and further study showed that OsNAC120 promotes GA biosynthesis by transcriptionally activating the GA biosynthetic genes OsGA20ox1 and OsGA20ox3. The DELLA protein SLENDER RICE1 (SLR1) interacts with OsNAC120 and impedes its transactivation ability, and GA treatment can remove the inhibition of transactivation activity caused by SLR1. On the other hand, OsNAC120 negatively regulates rice drought tolerance by repressing ABA-induced stomatal closure. Mechanistic investigation revealed that OsNAC120 inhibits ABA biosynthesis via transcriptional repression of the ABA biosynthetic genes OsNCED3 and OsNCED4. Rice OSMOTIC STRESS/ABA-ACTIVATED PROTEIN KINASE 9 (OsSAPK9) physically interacts with OsNAC120 and mediates its phosphorylation, which results in OsNAC120 degradation. ABA treatment accelerates OsNAC120 degradation and reduces its transactivation activity. Together, our findings provide evidence that OsNAC120 plays critical roles in balancing GA-mediated growth and ABA-induced drought tolerance in rice. This research will help us to understand the mechanisms underlying the trade-off between plant growth and stress tolerance and to engineer stress-resistant, high-yielding crops.

Characterization of sucrose nonfermenting-1-related protein kinase 2 (SnRK2) gene family in Haynaldia villosa demonstrated SnRK2.9-V enhances drought and salt stress tolerance of common wheat

BACKGROUND

The sucrose nonfermenting-1-related protein kinase 2 (SnRK2) plays a crucial role in responses to diverse biotic/abiotic stresses. Currently, there are reports on these genes in Haynaldia villosa, a diploid wild relative of wheat.

RESULTS

To understand the evolution of SnRK2-V family genes and their roles in various stress conditions, we performed genome-wide identification of the SnRK2-V gene family in H. villosa. Ten SnRK2-V genes were identified and characterized for their structures, functions and spatial expressions. Analysis of gene exon/intron structure further revealed the presence of evolutionary paths and replication events of SnRK2-V gene family in the H. villosa. In addition, the features of gene structure, the chromosomal location, subcellular localization of the gene family were investigated and the phylogenetic relationship were determined using computational approaches. Analysis of cis-regulatory elements of SnRK2-V gene members revealed their close correlation with different phytohormone signals. The expression profiling revealed that ten SnRK2-V genes expressed at least one tissue (leave, stem, root, or grain), or in response to at least one of the biotic (stripe rust or powdery mildew) or abiotic (drought or salt) stresses. Moreover, SnRK2.9-V was up-regulated in H. villosa under the drought and salt stress and overexpressing of SnRK2.9-V in wheat enhanced drought and salt tolerances via enhancing the genes expression of antioxidant enzymes, revealing a potential value of SnRK2.9-V in wheat improvement for salt tolerance.

CONCLUSION

Our present study provides a basic genome-wide overview of SnRK2-V genes in H. villosa and demonstrates the potential use of SnRK2.9-V in enhancing the drought and salt tolerances in common wheat.

The E3 ligase TaGW2 mediates transcription factor TaARR12 degradation to promote drought resistance in wheat

Drought stress limits crop yield, but the molecular modulators and their mechanisms underlying the trade-off between drought resistance and crop growth and development remain elusive. Here, a grain width and weight2 (GW2)-like really interesting new gene finger E3 ligase, TaGW2, was identified as a pivotal regulator of both kernel development and drought responses in wheat (Triticum aestivum). TaGW2 overexpression enhances drought resistance but leads to yield drag under full irrigation conditions. In contrast, TaGW2 knockdown or knockout attenuates drought resistance but remarkably increases kernel size and weight. Furthermore, TaGW2 directly interacts with and ubiquitinates the type-B Arabidopsis response regulator TaARR12, promoting its degradation via the 26S proteasome. Analysis of TaARR12 overexpression and knockdown lines indicated that TaARR12 represses the drought response but does not influence grain yield in wheat. Further DNA affinity purification sequencing combined with transcriptome analysis revealed that TaARR12 downregulates stress-responsive genes, especially group-A basic leucine zipper (bZIP) genes, resulting in impaired drought resistance. Notably, TaARR12 knockdown in the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated tagw2 knockout mutant leads to significantly higher drought resistance and grain yield compared to wild-type plants. Collectively, these findings show that the TaGW2-TaARR12 regulatory module is essential for drought responses, providing a strategy for improving stress resistance in high-yield wheat varieties.

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.

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.

Function identification of miR159a, a positive regulator during poplar resistance to drought stress

Drought seriously affects the growth and development of plants. MiR159 is a highly conserved and abundant microRNA family that plays a crucial role in plant growth and stress responses. However, studies of its function in woody plants are still lacking. Here, the expression of miR159a was significantly upregulated after drought treatment in poplar, and the overexpression of miR159a (OX159a) significantly reduced the open area of the stomata and improved water-use efficiency in poplar. After drought treatment, OX159a lines had better scavenging ability of reactive oxygen species and damage of the membrane system was less than that in wild-type lines. MYB was the target gene of miR159a, as verified by psRNATarget prediction, RT-qPCR, degradome sequencing, and 5' rapid amplification of cDNA ends (5' RACE). Additionally, miR159a-short tandem target mimic suppression (STTM) poplar lines showed increased sensitivity to drought stress. Transcriptomic analysis comparing OX159a lines with wild-type lines revealed upregulation of a series of genes related to response to water deprivation and metabolite synthesis. Moreover, drought-responsive miR172d and miR398 were significantly upregulated and downregulated respectively in OX159a lines. This investigation demonstrated that miR159a played a key role in the tolerance of poplar to drought by reducing stomata open area, increasing the number and total area of xylem vessels, and enhancing water-use efficiency, and provided new insights into the role of plant miR159a and crucial candidate genes for the molecular breeding of trees with tolerance to drought stress.

Roles of the pepper JAZ protein CaJAZ1-03 and its interacting partner RING-type E3 ligase CaASRF1 in regulating ABA signaling and drought responses

Plants have developed various defense mechanisms against environmental stresses by regulating hormone signaling. Jasmonic acid (JA) is a major phytohormone associated with plant defense responses. JASMONATE ZIM-DOMAIN (JAZ) proteins play a regulatory role in repressing JA signaling, impacting plant responses to both biotic and abiotic stresses. Here, we isolated 7 JAZ genes in pepper and selected CA03g31030, a Capsicum annuum JAZ1-03 (CaJAZ1-03) gene, for further study based on its expression level in response to abiotic stresses. Through virus-induced gene silencing (VIGS) in pepper and overexpression in transgenic Arabidopsis plants, we established the functional role of CaJAZ1-03. Functional studies revealed that CaJAZ1-03 dampens abscisic acid (ABA) signaling and drought stress responses. The cell-free degradation assay showed faster degradation of CaJAZ1-03 in drought- or ABA-treated pepper leaves compared to healthy leaves. Conversely, CaJAZ1-03 was completely preserved under MG132 treatment, indicating that CaJAZ1-03 stability is modulated via the ubiquitin-26s proteasome pathway. We also found that the pepper RING-type E3 ligase CaASRF1 interacts with and ubiquitinates CaJAZ1-03. Additional cell-free degradation assays revealed a negative correlation between CaJAZ1-03 and CaASRF1 expression levels. Collectively, these findings suggest that CaJAZ1-03 negatively regulates ABA signaling and drought responses and that its protein stability is modulated by CaASRF1.

RING finger ubiquitin E3 ligase CsCHYR1 targets CsATAF1 for degradation to modulate the drought stress response of cucumber through the ABA-dependent pathway

CsCHYR1 (CHY ZINC-FINGER AND RING PROTEIN1) encodes a RING (Really Interesting New Gene) finger E3 ubiquitin ligase involved in ubiquitin-mediated protein degradation and plays an important role for cucumber to resist drought stress. Here, we obtain one of the candidate proteins CsCHYR1 that probably interacts with CsATAF1 by yeast-two hybrid screening. Subsequently, it is verified that CsCHYR1 interacts with CsATAF1 and has self-ubiquitination activity. When the cysteine residue at 180 in the RING domain of CsCHYR1 is replaced by serine or alanine, ubiquitin could not be transported from E2 to the substrate. CsCHYR1 ubiquitinates CsATAF1 and affects the stability of CsATAF1 when plants are subjected to drought stress. The expression level of CsCHYR1 is increased by 4-fold after ABA treatment at 9 h. The Atchyr1 mutants perform an ABA-hyposensitive phenotype and have a lower survival rate than Col-0 and CsCHYR1 Atchyr1 lines. In addition, CsCHYR1 interacts with CsSnRK2.6. Therefore, our study reveals a CsSnRK2.6-CsCHYR1-CsATAF1 complex to promote the drought stress response by decreasing CsATAF1 protein accumulation and inducing stomatal closure. Those findings provide new ideas for cucumber germplasm innovation from the perspective of biochemistry and molecular biology.

The ubiquitin-protein ligase MIEL1 localizes to peroxisomes to promote seedling oleosin degradation and lipid droplet mobilization

Lipid droplets are organelles conserved across eukaryotes that store and release neutral lipids to regulate energy homeostasis. In oilseed plants, fats stored in seed lipid droplets provide fixed carbon for seedling growth before photosynthesis begins. As fatty acids released from lipid droplet triacylglycerol are catabolized in peroxisomes, lipid droplet coat proteins are ubiquitinated, extracted, and degraded. In Arabidopsis seeds, the predominant lipid droplet coat protein is OLEOSIN1 (OLE1). To identify genes modulating lipid droplet dynamics, we mutagenized a line expressing mNeonGreen-tagged OLE1 expressed from the OLE1 promoter and isolated mutants with delayed oleosin degradation. From this screen, we identified four miel1 mutant alleles. MIEL1 (MYB30-interacting E3 ligase 1) targets specific MYB transcription factors for degradation during hormone and pathogen responses [D. Marino et al., Nat. Commun. 4, 1476 (2013); H. G. Lee and P. J. Seo, Nat. Commun. 7, 12525 (2016)] but had not been implicated in lipid droplet dynamics. OLE1 transcript levels were unchanged in miel1 mutants, indicating that MIEL1 modulates oleosin levels posttranscriptionally. When overexpressed, fluorescently tagged MIEL1 reduced oleosin levels, causing very large lipid droplets. Unexpectedly, fluorescently tagged MIEL1 localized to peroxisomes. Our data suggest that MIEL1 ubiquitinates peroxisome-proximal seed oleosins, targeting them for degradation during seedling lipid mobilization. The human MIEL1 homolog (PIRH2; p53-induced protein with a RING-H2 domain) targets p53 and other proteins for degradation and promotes tumorigenesis [A. Daks et al., Cells 11, 1515 (2022)]. When expressed in Arabidopsis, human PIRH2 also localized to peroxisomes, hinting at a previously unexplored role for PIRH2 in lipid catabolism and peroxisome biology in mammals.

Haplotype-Resolution Transcriptome Analysis Reveals Important Responsive Gene Modules and Allele-Specific Expression Contributions under Continuous Salt and Drought in Camellia sinensis

The tea plant, Camellia sinensis (L.) O. Kuntze, is one of the most important beverage crops with significant economic and cultural value. Global climate change and population growth have led to increased salt and drought stress, negatively affecting tea yield and quality. The response mechanism of tea plants to these stresses remains poorly understood due to the lack of reference genome-based transcriptional descriptions. This study presents a high-quality genome-based transcriptome dynamic analysis of C. sinensis' response to salt and drought stress. A total of 2244 upregulated and 2164 downregulated genes were identified under salt and drought stress compared to the control sample. Most of the differentially expression genes (DEGs) were found to involve divergent regulation processes at different time points under stress. Some shared up- and downregulated DEGs related to secondary metabolic and photosynthetic processes, respectively. Weighted gene co-expression network analysis (WGCNA) revealed six co-expression modules significantly positively correlated with C. sinensis' response to salt or drought stress. The MEpurple module indicated crosstalk between the two stresses related to ubiquitination and the phenylpropanoid metabolic regulation process. We identified 1969 salt-responsive and 1887 drought-responsive allele-specific expression (ASE) genes in C. sinensis. Further comparison between these ASE genes and tea plant heterosis-related genes suggests that heterosis likely contributes to the adversity and stress resistance of C. sinensis. This work offers new insight into the underlying mechanisms of C. sinensis' response to salt and drought stress and supports the improved breeding of tea plants with enhanced salt and drought tolerance.

Ubiquitin E3 ligase AtCHYR2 functions in glucose regulation of germination and post-germinative growth in Arabidopsis thaliana

KEY MESSAGE

Cytoplasm-localized RING ubiquitin E3 ligase AtCHYR2 involved in plant glucose responses during germination and post-germinative growth. CHY ZINC FINGER AND RING PROTEIN (CHYR) containing both a CHY zinc finger and a C3H2C3-type RING domain plays important roles in plant drought tolerance and the abscisic acid (ABA) response; however, their functions in sugar signaling pathways are less studied. Here, we report a glucose (Glc) response gene AtCHYR2, a homolog of RZFP34/CHYR1, which is induced by various abiotic stresses, ABA, and sugar treatments. In vitro, we demonstrated that AtCHYR2 is a cytoplasm-localized RING ubiquitin E3 ligase. Overexpression of AtCHYR2 led to hypersensitivity to Glc and enhanced Glc-mediated inhibition of cotyledon greening and post-germinative growth. Contrastingly, AtCHYR2 loss-of-function plants were insensitive to Glc-regulated seed germination and primary root growth, suggesting that AtCHYR2 is a positively regulator of the plant glucose response. Additionally, physiological analyses showed that overexpression AtCHYR2 increased stomata aperture and photosynthesis under normal condition, and promoted accumulation of endogenous soluble sugar and starch in response to high Glc. Genome-wide RNA sequencing analysis showed that AtCHYR2 affects a major proportion of Glc-responsive genes. Particularly, sugar marker gene expression analysis suggested that AtCHYR2 enhances the Glc response via a signaling pathway dependent on glucose metabolism. Taken together, our findings show that a novel RING ubiquitin E3 ligase, AtCHYR2, plays an important role in glucose responses in Arabidopsis.

24-Epibrassinolide confers zinc stress tolerance in watermelon seedlings through modulating antioxidative capacities and lignin accumulation

Zinc (Zn) is an important element in plants, but over-accumulation of Zn is harmful. It is well-known that brassinolide (BR) plays a key role in the regulation of abiotic stress responses in plants. However, the effects of brassinolide on alleviating Zn phytotoxicity in watermelon (Citrullus lanatus L.) seedlings are not clear. The purpose of this study was to study the effect of 24-epibrassinolide (EBR, one of the bioactive BRs) on Zn tolerance of watermelon seedlings and its potential resistance mechanism. Exposure to excessive Zn significantly inhibited shoot and root fresh weight of watermelon, but this could be significantly alleviated by the optimum 0.05 μM EBR. Exogenous spraying EBR increased the pigments and alleviated oxidative damage caused by Zn through reducing Zn accumulation and the levels of reactive oxygen species (ROS) and malonaldehyde (MDA) and increasing the activities of antioxidant enzymes and contents of ascorbic acid (AsA) and glutathione (GSH). Importantly, the relative mRNA levels of antioxidant genesincluding Cu/Zn-superoxidedismutase (Cu-Zn SOD), catalase (CAT), ascorbic acid peroxidase (APX), and glutathione reductase (GR) were significantly induced after EBR treatment. In addition, EBR pre-treatment induced lignin accumulation under Zn stress, and the activity of phenylalanine ammonia-lyase (PAL) and 4-coumaric ligase (4CL), two key enzymes regulating lignin synthesis, also tended to be consistent. Collectively, the present research proves the beneficial effects of EBR in response to Zn stress through enhancing antioxidant defense and lignin accumulation and provides a new insight into the mechanism of BR-enhancing heavy metal tolerance.

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.

Growth-regulating factor 15-mediated gene regulatory network enhances salt tolerance in poplar

Soil salinity is an important determinant of crop productivity and triggers salt stress response pathways in plants. The salt stress response is controlled by transcriptional regulatory networks that maintain regulatory homeostasis through combinations of transcription factor (TF)-DNA and TF-TF interactions. We investigated the transcriptome of poplar 84 K (Populus alba × Populus glandulosa) under salt stress using samples collected at 4- or 6-h intervals within 2 days of salt stress treatment. We detected 24,973 differentially expressed genes, including 2,231 TFs that might be responsive to salt stress. To explore these interactions and targets of TFs in perennial woody plants, we combined gene regulatory networks, DNA affinity purification sequencing, yeast two-hybrid-sequencing, and multi-gene association approaches. Growth-regulating factor 15 (PagGRF15) and its target, high-affinity K+ transporter 6 (PagHAK6), were identified as an important regulatory module in the salt stress response. Overexpression of PagGRF15 and PagHAK6 in transgenic lines improved salt tolerance by enhancing Na+ transport and modulating H2O2 accumulation in poplar. Yeast two-hybrid assays identified more than 420 PagGRF15-interacting proteins, including ETHYLENE RESPONSE FACTOR TFs and a zinc finger protein (C2H2) that are produced in response to a variety of phytohormones and environmental signals and are likely involved in abiotic stress. Therefore, our findings demonstrate that PagGRF15 is a multifunctional TF involved in growth, development, and salt stress tolerance, highlighting the capability of a multifaceted approach in identifying regulatory nodes in plants.

A translatome-transcriptome multi-omics gene regulatory network reveals the complicated functional landscape of maize

BACKGROUND

Maize (Zea mays L.) is one of the most important crops worldwide. Although sophisticated maize gene regulatory networks (GRNs) have been constructed for functional genomics and phenotypic dissection, a multi-omics GRN connecting the translatome and transcriptome is lacking, hampering our understanding and exploration of the maize regulatome.

RESULTS

We collect spatio-temporal translatome and transcriptome data and systematically explore the landscape of gene transcription and translation across 33 tissues or developmental stages of maize. Using this comprehensive transcriptome and translatome atlas, we construct a multi-omics GRN integrating mRNAs and translated mRNAs, demonstrating that translatome-related GRNs outperform GRNs solely using transcriptomic data and inter-omics GRNs outperform intra-omics GRNs in most cases. With the aid of the multi-omics GRN, we reconcile some known regulatory networks. We identify a novel transcription factor, ZmGRF6, which is associated with growth. Furthermore, we characterize a function related to drought response for the classic transcription factor ZmMYB31.

CONCLUSIONS

Our findings provide insights into spatio-temporal changes across maize development at both the transcriptome and translatome levels. Multi-omics GRNs represent a useful resource for dissection of the regulatory mechanisms underlying phenotypic variation.

Genome assembly and genetic dissection of a prominent drought-resistant maize germplasm

In the context of climate change, drought is one of the most limiting factors that influence crop production. Maize, as a major crop, is highly vulnerable to water deficit, which causes significant yield loss. Thus, identification and utilization of drought-resistant germplasm are crucial for the genetic improvement of the trait. Here we report on a high-quality genome assembly of a prominent drought-resistant genotype, CIMBL55. Genomic and genetic variation analyses revealed that 65 favorable alleles of 108 previously identified drought-resistant candidate genes were found in CIMBL55, which may constitute the genetic basis for its excellent drought resistance. Notably, ZmRtn16, encoding a reticulon-like protein, was found to contribute to drought resistance by facilitating the vacuole H+-ATPase activity, which highlights the role of vacuole proton pumps in maize drought resistance. The assembled CIMBL55 genome provided a basis for genetic dissection and improvement of plant drought resistance, in support of global food security.

Overexpression of two CONSTANS-like 2 (MiCOL2) genes from mango delays flowering and enhances tolerance to abiotic stress in transgenic Arabidopsis

The CO/COL gene family plays an important role in regulating photoperiod-dependent flowering time in plants. In this study, two COL2 gene homologs, MiCOL2A and MiCOL2B, were isolated from 'SiJiMi' mango, and their expression patterns and functions were characterized. The MiCOL2A and MiCOL2B genes both belonged to the group Ⅰ of CO/COL gene family. MiCOL2A and MiCOL2B exhibited distinct circadian rhythms and were highly expressed in leaves during the flowering induction period. Subcellular localization analysis revealed that MiCOL2A and MiCOL2B are localized in the nucleus. The overexpression of MiCOL2A and MiCOL2B significantly delayed flowering time in Arabidopsis under both long-day (LD) and short-day (SD) conditions. The MiCOL2A and MiCOL2B overexpression Arabidopsis plants exhibited more tolerance to slat and drought stress after abiotic stress treatments, with greater ROS scavenging capacity and protective enzyme activity, less cell damage and death and higher expression of stress response genes than wild type plants. Bimolecular fluorescence complementation (BiFC) analysis showed that MiCOL2A and MiCOL2B interacted with several stress-related proteins, including zinc finger protein 4 (MiZFP4), MYB30-INTERACTING E3 LIGASE 1 (MiMIEL1) and RING zinc finger protein 34 (MiRZFP34). The results indicate that MiCOL2A and MiCOL2B are not only involved in flowering time but also play a positive role in abiotic stress responses in plants.

Evolutionary Analysis of StSnRK2 Family Genes and Their Overexpression in Transgenic Tobacco Improve Drought Tolerance

Sucrose non-ferment 1-related protein kinase 2 (SnRK2) is a highly conserved protein kinase in plants that plays an important role in regulating plant response to drought stress. Although it has been reported in some plants, the evolutionary relationship of potato SnRK2s and their function in drought resistance have not been systematically analyzed. In this study, molecular characteristic analysis showed that 8 StSnRK2s were distributed on six chromosomes, coding proteins were divided into three subgroups, and StSnRK2s clustered in the same subgroup had similar conserved motifs and domains. In addition, StSnRK2 has a wide range of replication events in some species, making it closer to dicots in the process of evolution. In addition, the average nonsynonymous substitution rate/synonymous substitution rate (Ka/Ks) value of SnRK2s in monocots was higher than that of dicots. The codon usage index showed that SnRK2s prefer to use cytosine 3 (C3s), guanine 3 (G3s) and GC content (GC3s) in monocots, whereas thymine 3 (T3s) and adenine 3 (A3s) are preferred in dicots. Furthermore, stress response analysis showed that the expression of StSnRK2s under different degrees of drought stress significantly correlated with one or more stress-related physiological indices, such as proline and malondialdehyde (MDA) content, superoxide dismutase (SOD) and catalase (CAT) activity, ion leakage (IL) etc. The drought resistance of StSnRK2 transgenic plants was determined to occur in the order of StSnRK2.1/2.8 > StSnRK2.2/2.5 > StSnRK2.4/2.6 > StSnRK2.3 > StSnRK2.7, was attributed to not only lower IL but also higher proline, soluble sugar contents and stress-related genes in transgenic plants compared to wild type (WT). In conclusion, this study provides useful insights into the evolution and function of StSnRK2s and lays a foundation for further study on the molecular mechanism of StSnRK2s regulating potato drought resistance.

Molecular evidence for adaptive evolution of drought tolerance in wild cereals

The considerable drought tolerance of wild cereal crop progenitors has diminished during domestication in the pursuit of higher productivity. Regaining this trait in cereal crops is essential for global food security but requires novel genetic insight. Here, we assessed the molecular evidence for natural variation of drought tolerance in wild barley (Hordeum spontaneum), wild emmer wheat (Triticum dicoccoides), and Brachypodium species collected from dry and moist habitats at Evolution Canyon, Israel (ECI). We report that prevailing moist vs dry conditions have differentially shaped the stomatal and photosynthetic traits of these wild cereals in their respective habitats. We present the genomic and transcriptomic evidence accounting for differences, including co-expression gene modules, correlated with physiological traits, and selective sweeps, driven by the xeric site conditions on the African Slope (AS) at ECI. Co-expression gene module 'circadian rhythm' was linked to significant drought-induced delay in flowering time in Brachypodium stacei genotypes. African Slope-specific differentially expressed genes are important in barley drought tolerance, verified by silencing Disease-Related Nonspecific Lipid Transfer 1 (DRN1), Nonphotochemical Quenching 4 (NPQ4), and Brassinosteroid-Responsive Ring-H1 (BRH1). Our results provide new genetic information for the breeding of resilient wheat and barley in a changing global climate with increasingly frequent drought events.

The JASMONATE ZIM-domain-OPEN STOMATA1 cascade integrates jasmonic acid and abscisic acid signaling to regulate drought tolerance by mediating stomatal closure in poplar

Drought, which directly affects the yield of crops and trees, is a natural stress with a profound impact on the economy. Improving water use efficiency (WUE) and drought tolerance are relatively effective strategies to alleviate drought stress. OPEN STOMATA1 (OST1), at the core of abscisic acid (ABA) signaling, can improve WUE by regulating stomatal closure and photosynthesis. Methyl jasmonate (MeJA) and ABA crosstalk is considered to be involved in the response to drought stress, but the detailed molecular mechanism is insufficiently known. Here, Populus euphratica, which naturally grows in arid and semiarid regions, was selected as the species for studying MeJA and ABA crosstalk under drought. A yeast two-hybrid assay was performed using PeOST1 as bait and a nucleus-localized factor, JASMONATE ZIM-domain protein 2 (PeJAZ2), was found to participate in MeJA signaling by interacting with PeOST1. Overexpression of PeJAZ2 in poplar notably increased water deficit tolerance and WUE in both severe and mild drought stress by regulating ABA signaling rather than ABA synthesis. Furthermore, a PeJAZ2 overexpression line was shown to have greater ABA-induced stomatal closure and hydrogen peroxide (H2O2) production. Collectively, this evidence establishes a mechanism in which PeJAZ2 acts as a positive regulator in response to drought stress via ABA-induced stomatal closure caused by H2O2 production. Our study presents a new insight into the crosstalk of ABA and jasmonic acid signaling in regulating WUE and drought stress, providing a basis of the drought tolerance mechanism of P. euphratica.

Identification and expression pattern analysis of the OsSnRK2 gene family in rice

Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) is a class of plant-specific serine/threonine (Ser/Thr) protein kinase that plays an important role in rice stress tolerance, growth and development. However, systematic bioinformatics and expression pattern analysis have not been reported. In the current study, ten OsSnRK2 genes were identified in the rice genome and located on 7 chromosomes, which can be classified into three subfamilies (I, II, and III). Many cis-regulatory elements were identified in the promoter region of OsSnRK2 genes, including hormone response elements, defense and stress responsive elements, indicating that the OsSnRK2 family may play a crucial role in response to hormonal and abiotic stress. Quantitative tissue analysis showed that OsSnRK2 genes expressed in all tissues of rice, but the expression abundance varied from different tissues and showed varietal variability. In addition, expression pattern of OsSnRK2 were analyzed under abiotic stress (salt, drought, salt and drought) and showed obvious difference in diverse abiotic stress. In general, these results provide useful information for understanding the OsSnRK2 gene family and analyzing its functions in rice in response to ABA, salt and drought stress, especially salt-drought combined stress.

RNAi and CRISPR-Cas silencing E3-RING ubiquitin ligase AIP2 enhances soybean seed protein content

The majority of plant protein in the world's food supply is derived from soybean (Glycine max). Soybean is a key protein source for global animal feed and is incorporated into plant-based foods for people, including meat alternatives. Soybean protein content is genetically variable and is usually inversely related to seed oil content. ABI3-interacting protein 2 (AIP2) is an E3-RING ubiquitin ligase that targets the seed-specific transcription factor ABI3. Silencing both soybean AIP2 genes (AIP2a and AIP2b) by RNAi enhanced seed protein content by up to seven percentage points, with no significant decrease in seed oil content. The protein content enhancement did not alter the composition of the seed storage proteins. Inactivation of either AIP2a or AIP2b by a CRISPR-Cas9-mediated mutation increased seed protein content, and this effect was greater when both genes were inactivated. Transactivation assays in transfected soybean hypocotyl protoplasts indicated that ABI3 changes the expression of glycinin, conglycinin, 2S albumin, and oleosin genes, indicating that AIP2 depletion increased seed protein content by regulating activity of the ABI3 transcription factor protein. These results provide an example of a gene-editing prototype directed to improve global food security and protein availability in soybean that may also be applicable to other protein-source crops.

Natural variations of ZmSRO1d modulate the trade-off between drought resistance and yield by affecting ZmRBOHC-mediated stomatal ROS production in maize

While crop yields have historically increased, drought resistance has become a major concern in the context of global climate change. The trade-off between crop yield and drought resistance is a common phenomenon; however, the underlying molecular modulators remain undetermined. Through genome-wide association study, we revealed that three non-synonymous variants in a drought-resistant allele of ZmSRO1d-R resulted in plasma membrane localization and enhanced mono-ADP-ribosyltransferase activity of ZmSRO1d toward ZmRBOHC, which increased reactive oxygen species (ROS) levels in guard cells and promoted stomatal closure. ZmSRO1d-R enhanced plant drought resilience and protected grain yields under drought conditions, but it led to yield drag under favorable conditions. In contrast, loss-of-function mutants of ZmRBOHC showed remarkably increased yields under well-watered conditions, whereas they showed compromised drought resistance. Interestingly, by analyzing 189 teosinte accessions, we found that the ZmSRO1d-R allele was present in teosinte but was selected against during maize domestication and modern breeding. Collectively, our work suggests that the allele frequency reduction of ZmSRO1d-R in breeding programs may have compromised maize drought resistance while increased yields. Therefore, introduction of the ZmSRO1d-R allele into modern maize cultivars would contribute to food security under drought stress caused by global climate change.

NUCLEAR TRANSPORT FACTOR 2-LIKE improves drought tolerance by modulating leaf water loss in alfalfa (Medicago sativa L.)

Drought is a major environmental factor that limits the production of alfalfa (Medicago sativa). In the present study, M. sativa NUCLEAR TRANSPORT FACTOR 2-LIKE (MsNTF2L) was identified as a nucleus-, cytoplasm-, and plasma membrane-localized protein. Its transcriptional expression was highly induced by ABA and drought stress. Overexpression of MsNTF2L in Arabidopsis resulted in hypersensitivity to ABA during both the seed germination and seedling growth stages. However, transgenic Arabidopsis plants exhibited enhanced tolerance to drought stress by reducing the levels of reactive oxygen species (ROS) and increasing the expression of stress/ABA-inducible genes. Consistently, analysis of MsNTF2L overexpression (OE) and RNA interference (RNAi) alfalfa plants revealed that MsNTF2L confers drought tolerance through promoting ROS scavenging, a decrease in stomatal density, ABA-induced stomatal closure, and epicuticular wax crystal accumulation. MsNTF2L highly affected epicuticular wax deposition, as a large group of wax biosynthesis and transport genes were influenced in the alfalfa OE and RNAi lines. Furthermore, transcript profiling of drought-treated alfalfa WT, OE, and RNAi plants showed a differential drought response for genes related to stress/ABA signaling, antioxidant defense, and photosynthesis. Taken together, these results reveal that MsNTF2L confers drought tolerance in alfalfa via modulation of leaf water loss (by regulating both stomata and wax deposition), antioxidant defense, and photosynthesis.

The histidine phosphotransfer AHP4 plays a negative role in Arabidopsis plant response to drought

Cytokinin plays an important role in plant stress responses via a multistep signaling pathway, involving the histidine phosphotransfer proteins (HPs). In Arabidopsis thaliana, the AHP2, AHP3 and AHP5 proteins are known to affect drought responses; however, the role of AHP4 in drought adaptation remains undetermined. In the present study, using a loss-of-function approach we showed that AHP4 possesses an important role in the response of Arabidopsis to drought. This is evidenced by the higher survival rates of ahp4 than wild-type (WT) plants under drought conditions, which is accompanied by the downregulated AHP4 expression in WT during periods of dehydration. Comparative transcriptome analysis of ahp4 and WT plants revealed AHP4-mediated expression of several dehydration- and/or abscisic acid-responsive genes involved in modulation of various physiological and biochemical processes important for plant drought acclimation. In comparison with WT, ahp4 plants showed increased wax crystal accumulation in stems, thicker cuticles in leaves, greater sensitivity to exogenous abscisic acid at germination, narrow stomatal apertures, heightened leaf temperatures during dehydration, and longer root length under osmotic stress. In addition, ahp4 plants showed greater photosynthetic efficiency, lower levels of reactive oxygen species, reduced electrolyte leakage and lipid peroxidation, and increased anthocyanin contents under drought, when compared with WT. These differences displayed in ahp4 plants are likely due to upregulation of genes that encode enzymes involved in reactive oxygen species scavenging and non-enzymatic antioxidant metabolism. Overall, our findings suggest that AHP4 plays a crucial role in plant drought adaptation.

Emerging roles of the ubiquitin-proteasome pathway in enhancing crop yield by optimizing seed agronomic traits

Ubiquitin-proteasome pathway has the potential to modulate crop productivity by influencing agronomic traits. Being sessile, the plant often uses the ubiquitin-proteasome pathway to maintain the stability of different regulatory proteins to survive in an ever-changing environment. The ubiquitin system influences plant reproduction, growth, development, responses to the environment, and processes that control critical agronomic traits. E3 ligases are the major players in this pathway, and they are responsible for recognizing and tagging the targets/substrates. Plants have a variety of E3 ubiquitin ligases, whose functions have been studied extensively, ranging from plant growth to defense strategies. Here we summarize three agronomic traits influenced by ubiquitination: seed size and weight, seed germination, and accessory plant agronomic traits particularly panicle architecture, tillering in rice, and tassels branch number in maize. This review article highlights some recent progress on how the ubiquitin system influences the stability/modification of proteins that determine seed agronomic properties like size, weight, germination and filling, and ultimately agricultural productivity and quality. Further research into the molecular basis of the aforementioned processes might lead to the identification of genes that could be modified or selected for crop development. Likewise, we also propose advances and future perspectives in this regard.

MaMYB4 is a negative regulator and a substrate of RING-type E3 ligases MaBRG2/3 in controlling banana fruit ripening

Fruit ripening is a complex developmental process, which is modulated by both transcriptional and post-translational events. Control of fruit ripening is important in maintaining moderate quality traits and minimizing postharvest deterioration. In this study, we discovered that the transcription factor MaMYB4 acts as a negative regulator of fruit ripening in banana. The protein levels of MaMYB4 decreased gradually with banana fruit ripening, paralleling ethylene production, and decline in firmness. DNA affinity purification sequencing combined with RNA-sequencing analyses showed that MaMYB4 preferentially binds to the promoters of various ripening-associated genes including ethylene biosynthetic and cell wall modifying genes. Furthermore, ectopic expression of MaMYB4 in tomato delayed tomato fruit ripening, which was accompanied by downregulation of ethylene biosynthetic and cell wall modifying genes. Importantly, two RING finger E3 ligases MaBRG2/3, whose protein accumulation increased progressively with fruit ripening, were found to interact with and ubiquitinate MaMYB4, contributing to decreased accumulation of MaMYB4 during fruit ripening. Transient overexpression of MaMYB4 and MaBRG2/3 in banana fruit ripening delayed or promoted fruit ripening by inhibiting or stimulating ethylene biosynthesis, respectively. Taken together, we demonstrate that MaMYB4 negatively modulates banana fruit ripening, and that MaMYB4 abundance could be regulated by protein ubiquitination, thus providing insights into the role of MaMYB4 in controlling fruit ripening at both transcriptional and post-translational levels.

Genome-wide analysis and functional characterization of CHYR gene family associated with abiotic stress tolerance in bread wheat (Triticum aestivum L.)

BACKGROUND

CHY zinc-finger and RING finger (CHYR) proteins have been functionally characterized in plant growth, development and various stress responses. However, the genome-wide analysis was not performed in wheat.

RESULTS

In this study, a total of 18 TaCHYR genes were identified in wheat and classified into three groups. All TaCHYR genes contained CHY-zinc finger, C3H2C3-type RING finger and zinc ribbon domains, and group III members included 1-3 hemerythrin domains in the N-terminus regions. TaCHYR genes in each group shared similar conserved domains distribution. Chromosomal location, synteny and cis-elements analysis of TaCHYRs were also analyzed. Real-time PCR results indicated that most of selected 9 TaCHYR genes exhibited higher expression levels in leaves during wheat seedling stage. All these TaCHYR genes were up-regulated after PEG treatment, and these TaCHYRs exhibited differential expression patterns in response to salt, cold and heat stress in seedling leaves. The growth of yeast cells expressing TaCHYR2.1, TaCHYR9.2 and TaCHYR11.1 were inhibited under salt and dehydration stress. Moreover, gene ontology (GO) annotation, protein interaction and miRNA regulatory network of TaCHYR genes were analyzed.

CONCLUSIONS

These results increase our understanding of CHYR genes and provide robust candidate genes for further functional investigations aimed at crop improvement.

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.

Roles of E3 Ubiquitin Ligases in Plant Responses to Abiotic Stresses

Plants are frequently exposed to a variety of abiotic stresses, such as those caused by salt, drought, cold, and heat. All of these stressors can induce changes in the proteoforms, which make up the proteome of an organism. Of the many different proteoforms, protein ubiquitination has attracted a lot of attention because it is widely involved in the process of protein degradation; thus regulates many plants molecular processes, such as hormone signal transduction, to resist external stresses. Ubiquitin ligases are crucial in substrate recognition during this ubiquitin modification process. In this review, the molecular mechanisms of plant responses to abiotic stresses from the perspective of ubiquitin ligases have been described. This information is critical for a better understanding of plant molecular responses to abiotic stresses.