Arabidopsis DREB2A-interacting proteins function as RING E3 ligases and negatively regulate plant drought stress-responsive gene expression

Research progress on plant stress-associated protein (SAP) family: Master regulators to deal with environmental stresses

Every year, unfavorable environmental factors significantly affect crop productivity and threaten food security. Plants are sessile; they cannot move to escape unfavorable environmental conditions, and therefore, they activate a variety of defense pathways. Among them are processes regulated by stress-associated proteins (SAPs). SAPs have a specific zinc finger domain (A20) at the N-terminus and either AN1 or C2H2 at the C-terminus. SAP proteins are involved in many biological processes and in response to various abiotic or biotic constraints. Most SAPs play a role in conferring transgenic stress resistance and are stress-inducible. The emerging field of SAPs in abiotic or biotic stress response regulation has attracted the attention of researchers. Although SAPs interact with various proteins to perform their functions, the exact mechanisms of these interactions remain incompletely understood. This review aims to provide a comprehensive understanding of SAPs, covering their diversity, structure, expression, and subcellular localization. SAPs play a pivotal role in enabling crosstalk between abiotic and biotic stress signaling pathways, making them essential for developing stress-tolerant crops without yield penalties. Collectively, understanding the complex regulation of SAPs in stress responses can contribute to enhancing tolerance against various environmental stresses through several techniques such as transgenesis, classical breeding, or gene editing.

Exploring therapeutic targets and molecular mechanisms for treating diabetes mellitus-associated heart failure with Qishen Yiqi dropping pills: A network pharmacology and bioinformatics approach

Diabetes mellitus (DM) and heart failure frequently coexist, presenting significant public health challenges. QiShenYiQi Dropping Pills (QSDP) are widely employed in the treatment of diabetes mellitus concomitant with heart failure (DM-HF). Nevertheless, the precise mechanisms underlying their efficacy have yet to be elucidated. Active ingredients and likely targets of QSDP were retrieved from the TCMSP and UniProt databases. Genes associated with DM-HF were pinpointed through searches in the GeneCards, OMIM, DisGeNET, and TTD databases. Differential genes connected to DM-HF were sourced from the GEO database. Enrichment analyses via gene ontology and Kyoto Encyclopedia of Genes and Genomes pathways, as well as immune infiltration assessments, were conducted using R software. Further analysis involved employing molecular docking strategies to explore the interactions between the identified targets and active substances in QSDP that are pertinent to DM-HF treatment. This investigation effectively discerned 108 active compounds and 257 targets relevant to QSDP. A protein-protein interaction network was constructed, highlighting 6 central targets for DM-HF treatment via QSDP. Gene ontology enrichment analysis predominantly linked these targets with responses to hypoxia, metabolism of reactive oxygen species, and cytokine receptor interactions. Analysis of Kyoto Encyclopedia of Genes and Genomes pathways demonstrated that these targets mainly participate in pathways linked to diabetic complications, such as AGE-RAGE signaling, dyslipidemia, arteriosclerosis, the HIF-1 signaling pathway, and the tumor necrosis factor signaling pathway. Further, immune infiltration analysis implied that QSDP's mechanism in treating DM-HF might involve immune-mediated inflammation and crucial signaling pathways. Additionally, molecular docking studies showed that the active substances in QSDP have strong binding affinities with these identified targets. This research presents a new model for addressing DM-HF through the use of QSDP, providing novel insights into incorporating traditional Chinese medicine (TCM) principles in the clinical treatment of DM-HF. The implications of these findings are substantial for both clinical application and further scientific inquiry.

Genome-Wide Identification and Characterization of U-Box Gene Family Members and Analysis of Their Expression Patterns in Phaseolus vulgaris L. under Cold Stress

The common bean (Phaseolus vulgaris L.) is an economically important food crop grown worldwide; however, its production is affected by various environmental stresses, including cold, heat, and drought stress. The plant U-box (PUB) protein family participates in various biological processes and stress responses, but the gene function and expression patterns of its members in the common bean remain unclear. Here, we systematically identified 63 U-box genes, including 8 tandem genes and 55 non-tandem genes, in the common bean. These PvPUB genes were unevenly distributed across 11 chromosomes, with chromosome 2 holding the most members of the PUB family, containing 10 PUB genes. The analysis of the phylogenetic tree classified the 63 PUB genes into three groups. Moreover, transcriptome analysis based on cold-tolerant and cold-sensitive varieties identified 4 differentially expressed PvPUB genes, suggesting their roles in cold tolerance. Taken together, this study serves as a valuable resource for exploring the functional aspects of the common bean U-box gene family and offers crucial theoretical support for the development of new cold-tolerant common bean varieties.

Comparative proteomics in tall fescue to reveal underlying mechanisms for improving Photosystem II thermotolerance during heat stress memory

BACKGROUND

The escalating impacts of global warming intensify the detrimental effects of heat stress on crop growth and yield. Among the earliest and most vulnerable sites of damage is Photosystem II (PSII). Plants exposed to recurring high temperatures develop heat stress memory, a phenomenon that enables them to retain information from previous stress events to better cope with subsequent one. Understanding the components and regulatory networks associated with heat stress memory is crucial for the development of heat-resistant crops.

RESULTS

Physiological assays revealed that heat priming (HP) enabled tall fescue to possess higher Photosystem II photochemical activity when subjected to trigger stress. To investigate the underlying mechanisms of heat stress memory, we performed comparative proteomic analyses on tall fescue leaves at S0 (control), R4 (primed), and S5 (triggering), using an integrated approach of Tandem Mass Tag (TMT) labeling and Liquid Chromatography-Mass Spectrometry. A total of 3,851 proteins were detected, with quantitative information available for 3,835 proteins. Among these, we identified 1,423 differentially abundant proteins (DAPs), including 526 proteins that were classified as Heat Stress Memory Proteins (HSMPs). GO and KEGG enrichment analyses revealed that the HSMPs were primarily associated with the "autophagy" in R4 and with "PSII repair", "HSP binding", and "peptidase activity" in S5. Notably, we identified 7 chloroplast-localized HSMPs (HSP21, DJC77, EGY3, LHCA4, LQY1, PSBR and DEGP8, R4/S0 > 1.2, S5/S0 > 1.2), which were considered to be effectors linked to PSII heat stress memory, predominantly in cluster 4. Protein-protein interaction (PPI) analysis indicated that the ubiquitin-proteasome system, with key nodes at UPL3, RAD23b, and UCH3, might play a role in the selective retention of memory effectors in the R4 stage. Furthermore, we conducted RT-qPCR validation on 12 genes, and the results showed that in comparison to the S5 stage, the R4 stage exhibited reduced consistency between transcript and protein levels, providing additional evidence for post-transcriptional regulation in R4.

CONCLUSIONS

These findings provide valuable insights into the establishment of heat stress memory under recurring high-temperature episodes and offer a conceptual framework for breeding thermotolerant crops with improved PSII functionality.

XBAT31 regulates reproductive thermotolerance through controlling the accumulation of HSFB2a/B2b under heat stress conditions

Heat shock transcription factors (HSFs) play a crucial role in heat stress tolerance in vegetative tissues. However, their involvement in reproductive tissues and their post-translational modifications are not well understood. In this study, we identify the E3 ligase XB3 ORTHOLOG 1 IN ARABIDOPSIS THALIANA (XBAT31) as a key player in the ubiquitination and degradation of HSFB2a/B2b. Our results show that the xbat31 mutant exhibits a higher percentage of unfertile siliques and decreased expression of HSPs in flowers under heat stress conditions compared to the wild type. Conversely, the hsfb2a hsfb2b double mutant displays improved reproductive thermotolerance. We find that XBAT31 interacts with HSFB2a/B2b and mediates their ubiquitination. Furthermore, HSFB2a/B2b ubiquitination is reduced in the xbat31-1 mutant, resulting in higher accumulation of HSFB2a/B2b in flowers under heat stress conditions. Overexpression of HSFB2a or HSFB2b leads to an increase in unfertile siliques under heat stress conditions. Thus, our results dissect the important role of the XBAT31-HSFB2a/B2b module in conferring reproductive thermotolerance in plants.

Arginine methylation of SM-LIKE PROTEIN 4 antagonistically affects alternative splicing during Arabidopsis stress responses

Arabidopsis (Arabidopsis thaliana) PROTEIN ARGININE METHYLTRANSFERASE5 (PRMT5) post-translationally modifies RNA-binding proteins by arginine (R) methylation. However, the impact of this modification on the regulation of RNA processing is largely unknown. We used the spliceosome component, SM-LIKE PROTEIN 4 (LSM4), as a paradigm to study the role of R-methylation in RNA processing. We found that LSM4 regulates alternative splicing (AS) of a suite of its in vivo targets identified here. The lsm4 and prmt5 mutants show a considerable overlap of genes with altered AS raising the possibility that splicing of those genes could be regulated by PRMT5-dependent LSM4 methylation. Indeed, LSM4 methylation impacts AS, particularly of genes linked with stress response. Wild-type LSM4 and an unmethylable version complement the lsm4-1 mutant, suggesting that methylation is not critical for growth in normal environments. However, LSM4 methylation increases with abscisic acid and is necessary for plants to grow under abiotic stress. Conversely, bacterial infection reduces LSM4 methylation, and plants that express unmethylable-LSM4 are more resistant to Pseudomonas than those expressing wild-type LSM4. This tolerance correlates with decreased intron retention of immune-response genes upon infection. Taken together, this provides direct evidence that R-methylation adjusts LSM4 function on pre-mRNA splicing in an antagonistic manner in response to biotic and abiotic stress.

COP1-ERF1-SCE1 regulatory module fine-tunes stress response under light-dark cycle in Arabidopsis

ETHYLENE RESPONSE FACTOR 1 (ERF1) plays an important role in integrating hormone crosstalk and stress responses. Previous studies have shown that ERF1 is unstable in the dark and its degradation is mediated by UBIQUITIN-CONJUGATING ENZYME 18. However, whether there are other enzymes regulating ERF1's stability remains unclear. Here, we use various in vitro and in vivo biochemical, genetic and stress-tolerance tests to demonstrate that both CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and SUMO-CONJUGATING ENZYME 1 (SCE1) regulate the stability of ERF1. We also performed transcriptomic analyses to understand their common regulatory pathways. We show that COP1 mediates ERF1 ubiquitination in the dark while SCE1 mediates ERF1 sumoylation in the light. ERF1 stability is positively regulated by SCE1 and negatively regulated by COP1. Upon abiotic stress, SCE1 plays a positive role in stress defence by regulating the expression of ERF1's downstream stress-responsive genes, whereas COP1 plays a negative role in stress response. Moreover, ERF1 also promotes photomorphogenesis and the expression of light-responsive genes. Our study reveals the molecular mechanism of how COP1 and SCE1 counteract to regulate ERF1's stability and light-stress signalling crosstalk.

GhUBC10-2 mediates GhGSTU17 degradation to regulate salt tolerance in cotton (Gossypium hirsutum)

Ubiquitin-conjugating enzyme (UBC) is a crucial component of the ubiquitin-proteasome system, which contributes to plant growth and development. While some UBCs have been identified as potential regulators of abiotic stress responses, the underlying mechanisms of this regulation remain poorly understood. Here, we report a cotton (Gossypium hirsutum) UBC gene, GhUBC10-2, which negatively regulates the salt stress response. We found that the gain of function of GhUBC10-2 in both Arabidopsis (Arabidopsis thaliana) and cotton leads to reduced salinity tolerance. Additionally, GhUBC10-2 interacts with glutathione S-transferase (GST) U17 (GhGSTU17), forming a heterodimeric complex that promotes GhGSTU17 degradation. Intriguingly, GhUBC10-2 can be self-polyubiquitinated, suggesting that it possesses E3-independent activity. Our findings provide new insights into the PTM of plant GST-mediated salt response pathways. Furthermore, we found that the WRKY transcription factor GhWRKY13 binds to the GhUBC10-2 promoter and suppresses its expression under salt conditions. Collectively, our study unveils a regulatory module encompassing GhWRKY13-GhUBC10-2-GhGSTU17, which orchestrates the modulation of reactive oxygen species homeostasis to enhance salt tolerance.

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

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

Regulatory networks in plant responses to drought and cold stress

Drought and cold represent distinct types of abiotic stress, each initiating unique primary signaling pathways in response to dehydration and temperature changes, respectively. However, a convergence at the gene regulatory level is observed where a common set of stress-responsive genes is activated to mitigate the impacts of both stresses. In this review, we explore these intricate regulatory networks, illustrating how plants coordinate distinct stress signals into a collective transcriptional strategy. We delve into the molecular mechanisms of stress perception, stress signaling, and the activation of gene regulatory pathways, with a focus on insights gained from model species. By elucidating both the shared and distinct aspects of plant responses to drought and cold, we provide insight into the adaptive strategies of plants, paving the way for the engineering of stress-resilient crop varieties that can withstand a changing climate.

E3 ubiquitin ligase TaSDIR1-4A activates membrane-bound transcription factor TaWRKY29 to positively regulate drought resistance

Drought is a deleterious abiotic stress factor that constrains crop growth and development. Post-translational modification of proteins mediated by the ubiquitin-proteasome system is an effective strategy for directing plant responses to stress, but the regulatory mechanisms in wheat remain unclear. In this study, we showed that TaSDIR1-4A is a positive modulator of the drought response. Overexpression of TaSDIR1-4A increased the hypersensitivity of stomata, root length and endogenous abscisic acid (ABA) content under drought conditions. TaSDIR1-4A encodes a C3H2C3-type RING finger protein with E3 ligase activity. Amino acid mutation in its conserved domain led to loss of activity and altered the subcellular localization. The membrane-bound transcription factor TaWRKY29 was identified by yeast two-hybrid screening, and it was confirmed as interacting with TaSDIR1-4A both in vivo and in vitro. TaSDIR1-4A mediated the polyubiquitination and proteolysis of the C-terminal amino acid of TaWRKY29, and its translocation from the plasma membrane to the nucleus. Activated TaWRKY29 bound to the TaABI5 promoter to stimulate its expression, thereby positively regulating the ABA signalling pathway and drought response. Our findings demonstrate the positive role of TaSDIR1-4A in drought tolerance and provide new insights into the involvement of UPS in the wheat stress response.

Identification and Characterization of the AREB/ABF Gene Family in Three Orchid Species and Functional Analysis of DcaABI5 in Arabidopsis

AREB/ABF (ABA response element binding) proteins in plants are essential for stress responses, while our understanding of AREB/ABFs from orchid species, important traditional medicinal and ornamental plants, is limited. Here, twelve AREB/ABF genes were identified within three orchids' complete genomes and classified into three groups through phylogenetic analysis, which was further supported with a combined analysis of their conserved motifs and gene structures. The cis-element analysis revealed that hormone response elements as well as light and stress response elements were widely rich in the AREB/ABFs. A prediction analysis of the orchid ABRE/ABF-mediated regulatory network was further constructed through cis-regulatory element (CRE) analysis of their promoter regions. And it revealed that several dominant transcriptional factor (TF) gene families were abundant as potential regulators of these orchid AREB/ABFs. Expression profile analysis using public transcriptomic data suggested that most AREB/ABF genes have distinct tissue-specific expression patterns in orchid plants. Additionally, DcaABI5 as a homolog of ABA INSENSITIVE 5 (ABI5) from Arabidopsis was selected for further analysis. The results showed that transgenic Arabidopsis overexpressing DcaABI5 could rescue the ABA-insensitive phenotype in the mutant abi5. Collectively, these findings will provide valuable information on AREB/ABF genes in orchids.

Gene pyramiding for boosted plant growth and broad abiotic stress tolerance

Abiotic stresses such as salinity, heat and drought seriously impair plant growth and development, causing a significant loss in crop yield and ornamental value. Biotechnology approaches manipulating specific genes prove to be effective strategies in crop trait modification. The Arabidopsis vacuolar pyrophosphatase gene AVP1, the rice SUMO E3 ligase gene OsSIZ1 and the cyanobacterium flavodoxin gene Fld have previously been implicated in regulating plant stress responses and conferring enhanced tolerance to different abiotic stresses when individually overexpressed in various plant species. We have explored the feasibility of combining multiple favourable traits brought by individual genes to acquire superior plant performance. To this end, we have simultaneously introduced AVP1, OsSIZ1 and Fld in creeping bentgrass. Transgenic (TG) plants overexpressing these three genes performed significantly better than wild type controls and the TGs expressing individual genes under both normal and various abiotic stress conditions, exhibited significantly enhanced plant growth and tolerance to drought, salinity and heat stresses as well as nitrogen and phosphate starvation, which were associated with altered physiological and biochemical characteristics and delicately fine-tuned expression of genes involved in plant stress responses. Our results suggest that AVP1, OsSIZ1 and Fld function synergistically to regulate plant development and plant stress response, leading to superior overall performance under both normal and adverse environments. The information obtained provides new insights into gene stacking as an effective approach for plant genetic engineering. A similar strategy can be extended for the use of other beneficial genes in various crop species for trait modifications, enhancing agricultural production.

Complex plant responses to drought and heat stress under climate change

Global climate change is predicted to result in increased yield losses of agricultural crops caused by environmental conditions. In particular, heat and drought stress are major factors that negatively affect plant development and reproduction, and previous studies have revealed how these stresses induce plant responses at physiological and molecular levels. Here, we provide a comprehensive overview of current knowledge concerning how drought, heat, and combinations of these stress conditions affect the status of plants, including crops, by affecting factors such as stomatal conductance, photosynthetic activity, cellular oxidative conditions, metabolomic profiles, and molecular signaling mechanisms. We further discuss stress-responsive regulatory factors such as transcription factors and signaling factors, which play critical roles in adaptation to both drought and heat stress conditions and potentially function as 'hubs' in drought and/or heat stress responses. Additionally, we present recent findings based on forward genetic approaches that reveal natural variations in agricultural crops that play critical roles in agricultural traits under drought and/or heat conditions. Finally, we provide an overview of the application of decades of study results to actual agricultural fields as a strategy to increase drought and/or heat stress tolerance. This review summarizes our current understanding of plant responses to drought, heat, and combinations of these stress conditions.

Comprehensive Characterization of the C3HC4 RING Finger Gene Family in Potato (Solanum tuberosum L.): Insights into Their Involvement in Anthocyanin Biosynthesis

The C3HC4 RING finger gene (RING-HC) family is a zinc finger protein crucial to plant growth. However, there have been no studies on the RING-HC gene family in potato. In this study, 77 putative StRING-HCs were identified in the potato genome and grouped into three clusters based on phylogenetic relationships, the chromosome distribution, gene structure, conserved motif, gene duplication events, and synteny relationships, and cis-acting elements were systematically analyzed. By analyzing RNA-seq data of potato cultivars, the candidate StRING-HC genes that might participate in tissue development, abiotic stress, especially drought stress, and anthocyanin biosynthesis were further determined. Finally, a StRING-HC gene (Soltu.DM.09G017280 annotated as StRNF4-like), which was highly expressed in pigmented potato tubers was focused on. StRNF4-like localized in the nucleus, and Y2H assays showed that it could interact with the anthocyanin-regulating transcription factors (TFs) StbHLH1 of potato tubers, which is localized in the nucleus and membrane. Transient assays showed that StRNF4-like repressed anthocyanin accumulation in the leaves of Nicotiana tabacum and Nicotiana benthamiana by directly suppressing the activity of the dihydroflavonol reductase (DFR) promoter activated by StAN1 and StbHLH1. The results suggest that StRNF4-like might repress anthocyanin accumulation in potato tubers by interacting with StbHLH1. Our comprehensive analysis of the potato StRING-HCs family contributes valuable knowledge to the understanding of their functions in potato development, abiotic stress, hormone signaling, and anthocyanin biosynthesis.

Arabidopsis thaliana ubiquitin-associated protein 2 (AtUAP2) functions as an E4 ubiquitin factor and negatively modulates dehydration stress response

E4, a ubiquitin (Ub) chain assembly factor and post-translational modification protein, plays a key role in the regulation of multiple cellular functions in plants during biotic or abiotic stress. We have more recently reported that E4 factor AtUAP1 is a negative regulator of the osmotic stress response and enhances the multi-Ub chain assembly of E3 ligase Arabidopsis thaliana RING Zinc Finger 1 (AtRZF1). To further investigate the function of other E4 Ub factors in osmotic stress, we isolated AtUAP2, an AtUAP1 homolog, which interacted with AtRZF1, using pull-down assay and bimolecular fluorescence complementation analysis. AtUAP2, a Ub-associated motif-containing protein, interacts with oligo-Ub5, -Ub6, and -Ub7 chains. The yeast functional complementation experiment revealed that AtUAP2 functions as an E4 Ub factor. In addition, AtUAP2 is localized in the cytoplasm, different from AtUAP1. The activity of AtUAP2 was relatively strongly induced in the leaf tissue of AtUAP2 promoter-β-glucuronidase transgenic plants by abscisic acid, dehydration, and oxidative stress. atuap2 RNAi lines were more insensitive to osmotic stress condition than wild-type during the early growth of seedlings, whereas the AtUAP2-overexpressing line exhibited relatively more sensitive responses. Analyses of molecular and physiological experiments showed that AtUAP2 could negatively mediate the osmotic stress-induced signaling. Genetic studies showed that AtRZF1 mutation could suppress the dehydration-induced sensitive phenotype of the AtUAP2-overexpressing line, suggesting that AtRZF1 acts genetically downstream of AtUAP2 during osmotic stress. Taken together, our findings show that the AtRZF1-AtUAP2 complex may play important roles in the ubiquitination pathway, which controls the osmotic stress response in Arabidopsis.

Genome-wide association study identifies a novel BMI1A QTL allele that confers FLC expression diversity in Arabidopsis thaliana

Identification and understanding of the genetic basis of natural variations in plants are essential for comprehending their phenotypic adaptation. Here, we report a genome-wide association study (GWAS) of FLOWERING LOCUS C (FLC) expression in 727 Arabidopsis accessions. We identified B LYMPHOMA MOLONEY MURINE LEUKEMIA VIRUS INSERTION REGION 1 HOMOLOG 1A (BMI1A) as a causal gene for one of the FLC expression quantitative trait loci (QTLs). Loss of function in BMI1A increases FLC expression and delays flowering time at 16 °C significantly compared with the wild type (Col-0). BMI1A activity is required for histone H3 lysine 27 trimethylation (H3K27me3) accumulation at the FLC, MADS AFFECTING FLOWERING 4 (MAF4), and MAF5 loci at low ambient temperature. We further uncovered two BMI1A haplotypes associated with the natural variation in FLC expression and flowering time at 16 °C, and demonstrated that polymorphisms in the BMI1A promoter region are the main contributor. Different BMI1A haplotypes are strongly associated with geographical distribution, and the low ambient temperature-sensitive BMI1A variants are associated with a lower mean temperature of the driest quarter of their collection sites compared with the temperature-non-responsive variants, indicating that the natural variations in BMI1A have adaptive functions in FLC expression and flowering time regulation. Therefore, our results provide new insights into the natural variations in FLC expression and flowering time diversity in plants.

Tobacco NtUBC1 and NtUBQ2 enhance salt tolerance by reducing sodium accumulation and oxidative stress through proteasome activation in Arabidopsis

The ubiquitin/proteasome system plays a crucial role in the regulation of plant responses to environmental stress. Here, we studied the involvement of the UBC1 and UBQ2 genes encoding a ubiquitin conjugating enzyme (E2) and ubiquitin extension protein, respectively, in the response to salt stress. Our results showed that the constitutive expression of tobacco NtUBC1 and NtUBQ2 in Arabidopsis thaliana improved salt tolerance, along with the lower Na+ level and higher K+/Na+ ratio compared to control plants. Moreover, the expression levels of sodium transporters, including AtHKT1 (High-Affinity K+ Transporter1) and AtSOS1 (Salt Overly Sensitive 1), were higher in NtUBC1- and NtUBQ2-Arabidopsis. However, the transcript level of AtNHX1 (Na+/H+ Exchanger 1) was similar between control and transgenic plants. After salt exposure, the activity of the 26S proteasome markedly increased in NtUBC1- and NtUBQ2-expressing plants; however, ubiquitinated protein levels decreased compared to control plants. Furthermore, higher activity of antioxidant enzymes and lower ROS production were observed in UBC1- and UBQ2-expressing plants. We further challenged atubc1, atubc2, and atubq2 single mutants and atubc1ubc2 double mutant lines with salt stress; interestingly, the salt sensitivity and sodium levels of the studied mutants were enhanced, while the potassium levels were reduced. However, the atubc1ubc2 double mutant illustrated a more severe phenotype than the single mutants, probably due to the redundant function of UBC1 and UBC2 in Arabidopsis. Taken together, NtUBC1 and NtUBQ2 enhance salt tolerance by enhancing 26S proteasome activity and reducing Na+ accumulation, ROS, and ubiquitinated/salt-denatured proteins.

APETALA2/ethylene-responsive factors in higher plant and their roles in regulation of plant stress response

Plants, anchored throughout their life cycles, face a unique set of challenges from fluctuating environments and pathogenic assaults. Central to their adaptative mechanisms are transcription factors (TFs), particularly the AP2/ERF superfamily-one of the most extensive TF families unique to plants. This family plays instrumental roles in orchestrating diverse biological processes ranging from growth and development to secondary metabolism, and notably, responses to both biotic and abiotic stresses. Distinguished by the presence of the signature AP2 domain or its responsiveness to ethylene signals, the AP2/ERF superfamily has become a nexus of research focus, with increasing literature elucidating its multifaceted roles. This review provides a synoptic overview of the latest research advancements on the AP2/ERF family, spanning its taxonomy, structural nuances, prevalence in higher plants, transcriptional and post-transcriptional dynamics, and the intricate interplay in DNA-binding and target gene regulation. Special attention is accorded to the ethylene response factor B3 subgroup protein Pti5 and its role in stress response, with speculative insights into its functionalities and interaction matrix in tomatoes. The overarching goal is to pave the way for harnessing these TFs in the realms of plant genetic enhancement and novel germplasm development.

Proteome Analysis of the ROF-FKBP Mutants Reveals Functional Relations among Heat Stress Responses, Plant Development, and Protein Quality Control during Heat Acclimation in Arabidopsis thaliana

In the present study, a differential screening following heat stress acclimation was performed in Arabidopsis thaliana WT and ROF-FKBP mutated plants using mass spectrometry, and the results were used to understand and analyze the effect of the ROF PPIases during thermotolerance acquisition in plants. Our data highlight the central role of these two PPIases in heat stress and point to their direct or indirect effect on other proteins participating in cellular functions such as protein folding and quality control, cell division, photosynthesis, and other metabolic and signaling processes. Specifically, the heat stress response, protein folding, and protein ER processing pathways are enhanced following a 37 °C acclimation period independent of the mutation state. However, at 37 °C, and in the double-mutated rof1-/2- plants, a higher accumulation of proteins belonging to the above pathways is observed compared with all other conditions (WT, single mutants, control, and heat-acclimated plants). Furthermore, the proteasomal pathway, involving the common member of both the protasomal and the lysosomal degradation pathway, CDC48, is over-represented in the extracts of both the untreated and heat-stressed rof1-/2- mutants compared with the other extracts. In contrast, in the single rof1- mutation, the heat acclimation pathway is suppressed at 37 °C when compared to the WT. Protein accumulation related to the heat stress and the protein quality control pathways points to a differential but also synergistic role of the two proteins. Protein complexes of other biochemical and developmental mechanisms, such as the light-harvesting complex of the photosynthetic pathway and the phosphoinositide binding proteins involved in membrane-trafficking events during cell plate formation and cytokinesis (patellin 1, 2, and 4), are negatively regulated in the rof1-/2- mutant. Our results suggest that ROF1 and ROF2 FKBPs regulate stress response, and developmental and metabolic pathways via a complex feedback mechanism involving partners that ensure protein quality control and plant survival during heat stress.

MePP2C24, a cassava (Manihot esculenta) gene encoding protein phosphatase 2C, negatively regulates drought stress and abscisic acid responses in transgenic Arabidopsis thaliana

Abscisic acid (ABA) signaling plays a crucial role in plant development and response to abiotic/biotic stress. However, the function and regulation of protein phosphatase 2C (PP2C), a key component of abscisic acid signaling, under abiotic stress are still unknown in cassava, a drought-tolerant crop. In this study, a cassava PP2C gene (MePP2C24) was cloned and characterized. The MePP2C24 transcripts increased in response to mannitol, NaCl, and ABA. Overexpression of MePP2C24 in Arabidopsis resulted in increased sensitivity to drought stress and decreased sensitivity to exogenous ABA. This was demonstrated by transgenic lines having higher levels of malondialdehyde (MDA), ion leakage (IL), and reactive oxygen species (ROS), lower activities of catalase (CAT) and peroxidase (POD), and lower proline content than wild type (WT) under drought stress. Moreover, MePP2C24 overexpression caused decrease in expression of drought-responsive genes related to ABA signaling pathway. In addition, MePP2C24 was localized in the cell nucleus and showed self-activation. Furthermore, many MePYLs (MePYL1, MePYL4, MePYL7-9, and MePYL11-13) could interact with MePP2C24 in the presence of ABA, and MePYL1 interacted with MePP2C24 in both the presence and absence of ABA. Additionally, MebZIP11 interacted with the promoter of MePP2C24 and exerted a suppressive effect. Taken together, our results suggest that MePP2C24 acts as a negative regulator of drought tolerance and ABA response.

NFXL1 functions as a transcriptional activator required for thermotolerance at reproductive stage in Arabidopsis

Plants are highly susceptible to abiotic stresses, particularly heat stress during the reproductive stage. However, the specific molecular mechanisms underlying this sensitivity remain largely unknown. In the current study, we demonstrate that the Nuclear Transcription Factor, X-box Binding Protein 1-Like 1 (NFXL1), directly regulates the expression of DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 2A (DREB2A), which is crucial for reproductive thermotolerance in Arabidopsis. NFXL1 is upregulated by heat stress, and its mutation leads to a reduction in silique length (seed number) under heat stress conditions. RNA-Seq analysis reveals that NFXL1 has a global impact on the expression of heat stress responsive genes, including DREB2A, Heat Shock Factor A3 (HSFA3) and Heat Shock Protein 17.6 (HSP17.6) in flower buds. Interestingly, NFXL1 is enriched in the promoter region of DREB2A, but not of either HSFA3 or HSP17.6. Further experiments using electrophoretic mobility shift assay have confirmed that NFXL1 directly binds to the DNA fragment derived from the DREB2A promoter. Moreover, effector-reporter assays have shown that NFXL1 activates the DREB2A promoter. The DREB2A mutants are also heat stress sensitive at the reproductive stage, and DEREB2A is epistatic to NFXL1 in regulating thermotolerance in flower buds. It is known that HSFA3, a direct target of DREB2A, regulates the expression of heat shock proteins genes under heat stress conditions. Thus, our findings establish NFXL1 as a critical upstream regulator of DREB2A in the transcriptional cassette responsible for heat stress responses required for reproductive thermotolerance in Arabidopsis.

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.

Genome-wide analysis of AP2/ERF gene and functional analysis of CqERF24 gene in drought stress in quinoa

Quinoa is a crop with high nutritional value and strong stress resistance. AP2/ERF transcription factors play a key role in plant growth and development. In this study, 148 AP2/ERF genes were identified in quinoa, which were divided into 5 subfamilies, including ERF, AP2, DREB, RAV and Soloist. The results showed that the number of introns ranged from 0 to 11, and the Motif 1-Motif 4 was highly conserved in most CqAP2/ERF proteins. The 148 CqAP2/ERF genes were distributed on 19 chromosomes. There were 93 pairs of duplicating genes in this family, and gene duplication played a critical role in the expansion of this family. Protein-protein interaction indicated that the proteins in CqAP2/ERF subfamily exhibited complex interactions, and GO enrichment analysis indicated that 148 CqAP2/ERF proteins were involved in transcription factor activity. In addition, CqAP2/ERF gene contains a large number of elements related to hormones in promoter region (IAA, GA, SA, ABA and MeJA) and stresses (salt, drought, low temperature and anaerobic induction). Transcriptome analysis under drought stress indicated that most of the CqAP2/ERF genes were responsive to drought stress, and subcellular localization indicated that CqERF24 was location in the nucleus, qRT-PCR results also showed that most of the genes such as CqERF15, CqERF24, CqDREB03, CqDREB14, CqDREB37 and CqDREB43 also responded to drought stress in roots and leaves. Overexpression of CqERF24 in Arabidopsis thaliana enhanced drought resistance by increasing antioxidant enzyme activity and activation-related stress genes, and the gene is sensitive to ABA, while silencing CqERF24 in quinoa decreased drought tolerance. In addition, overexpression of CqERF24 in quinoa calli enhanced resistance to mannitol. These results lay a solid foundation for further study on the role of AP2/ERF family genes in quinoa under drought stress.

The MADS-box family gene PtrANR1 encodes a transcription activator promoting root growth and enhancing plant tolerance to drought stress

KEY MESSAGE

PtrANR1 positively regulates plant drought tolerance by increasing proline level and reducing ROS accumulation. PtrANR1 directly activates PtrAUX1 expression to promote root growth and improve plant drought tolerance. Citrus quality and yield are severely declined under drought stress. To date, the effects of MADS-box family transcription factors (TFs) on plant drought resistance have made some progress. However, whether MADS-box family TFs are associated with citrus drought response has remained unclear. The current paper identified a MADS-box family gene PtrANR1 encoding anthocyanidin reductase from trifoliate orange. PtrANR1 exhibits high identities with ANR1 proteins found in various plants. PtrANR1 possesses two conserved domains known as MADS and kertanin-like domains. PtrANR1 is a nuclear protein which has transactivation activity. A significant induction of PtrANR1 transcript was detected in leaves and roots of trifoliate orange treated with PEG6000 and ABA. Under drought stress, Arabidopsis ectopic overexpressing PtrANR1 exhibited obviously elevated contents of proline, ABA and IAA, better developed root, enhanced antioxidant enzyme activities, as well as notably reduced accumulation of malondialdehyde (MDA) and reactive oxygen species (ROS) compared with WT plants. However, opposite change trends of these physiological indices were detected in PtrANR1 homolog silencing lemon. Furthermore, transgenic Arabidopsis displayed significantly increased expression levels in genes associated with ABA, IAA and proline production, IAA polar transport, ROS elimination and drought response. However, these genes exhibited noticeably decreased transcript levels in PtrANR1 homolog silencing lemon. Moreover, PtrANR1 could increase IAA content and promote root growth by binding to GArG-box in the promoter of PtrAUX1 to activate its transcript. These findings indicated that PtrANR1 had a beneficial impact on plant drought resistance through promoting root development, increasing proline accumulation and scavenging of ROS.

Gene mining and genomics-assisted breeding empowered by the pangenome of tea plant Camellia sinensis

Tea is one of the world's oldest crops and is cultivated to produce beverages with various flavours. Despite advances in sequencing technologies, the genetic mechanisms underlying key agronomic traits of tea remain unclear. In this study, we present a high-quality pangenome of 22 elite cultivars, representing broad genetic diversity in the species. Our analysis reveals that a recent long terminal repeat burst contributed nearly 20% of gene copies, introducing functional genetic variants that affect phenotypes such as leaf colour. Our graphical pangenome improves the efficiency of genome-wide association studies and allows the identification of key genes controlling bud flush timing. We also identified strong correlations between allelic variants and flavour-related chemistries. These findings deepen our understanding of the genetic basis of tea quality and provide valuable genomic resources to facilitate its genomics-assisted breeding.

Identification and Expression Analysis of the Alfin-like Gene Family in Tomato and the Role of SlAL3 in Salt and Drought Stresses

Alfin-like (AL) transcription factors are a family of plant-specific genes with a PHD-finger-like structural domain at the C-terminus and a DUF3594 structural domain at the N-terminus that play important roles in plant development and stress response. In the present study, genome-wide identification and analysis were performed of the AL protein family in cultivated tomato (Solanum lycopersicum) and three wild relatives (S. pennellii, S. pimpinellifolium, and S. lycopersicoides) to evaluate their response to different abiotic stresses. A total of 39 ALs were identified and classified into four groups and based on phylogenetic tree and evolutionary analysis were shown to have formed prior to the differentiation of monocotyledons and dicots. Moreover, cis-acting element analysis revealed that various phytohormone response and abiotic stress response elements were highly existed in tomato. In addition, further analysis of the SlAL3 gene revealed that its expression was induced by drought and salt stresses and localized to the nucleus. In conclusion, our findings concerning AL genes provide useful information for further studies on their functions and regulatory mechanisms and provide theoretical references for studying AL gene response to abiotic stresses in plants.

The DREB transcription factor, a biomacromolecule, responds to abiotic stress by regulating the expression of stress-related genes

Abiotic stress is a crucial factor that affects plant survival and growth and even leads to plant death in severe cases. Transcription factors can enhance the ability of plants to fight against various stresses by controlling the expression of downstream genes. The dehydration response element binding protein (DREB) is the most extensive subfamily of AP2/ERF transcription factors involved in abiotic stress. However, insufficient research on the signal network of DREB transcription factors has limited plant growth and reproduction. Furthermore, field planting of DREB transcription factors and their roles under multiple stress also require extensive research. Previous reports on DREB transcription factors have focused on the regulation of DREB expression and its roles in plant abiotic stress. In recent years, there has been new progress in DREB transcription factors. Here, the structure and classification, evolution and regulation, role in abiotic stress, and application in crops of DREB transcription factors were reviewed. And this paper highlighted the evolution of DREB1/CBF, as well as the regulation of DREB transcription factors under the participation of plant hormone signals and the roles of subgroups in abiotic stress. In the future, it will lay a solid foundation for further study of DREB transcription factors and pave the way for the cultivation of resistant plants.

Genome-wide identification and expression analysis of the Pisum sativum (L.) APETALA2/ethylene-responsive factor (AP2/ERF) gene family reveals functions in drought and cold stresses

AP2/ERF (APETALA2/Ethylene Response Factor) is a family of transcription factors that play essential roles in regulating gene expression in response to various environmental stimuli, including biotic and abiotic stresses, hormone signaling, and developmental processes. Pisum sativum (L.), commonly known as garden pea, is a winter crop sensitive to high temperatures and can also be affected by extreme cold and drought conditions. This study performed a genome-wide analysis of AP2/ERF genes and identified 153 AP2/ERF genes in P. sativum. Based on the conserved AP2/ERF domain and sequence homology, they were classified into AP2 (APETALA2), ERF (Ethylene Response Factor), DREB (Dehydration responsive element-binding), RAV (Related to Abscisic Acid Insensitive 3/ Viviparous 1) and Soloist subfamily. The DREB and ERF subfamily were further divided into groups A1-6 and B1-B6. Tandem and segmental duplication events were more frequent in the ERF subfamily, which can have important implications for their evolution and functional diversification. Under cold stress, the expression of DREB1A was highly induced in leaves, whereas DREB1B was suppressed. Similarly, the DREB2A, DREB2C, DREB2E, and DREB2F were induced in leaves under drought stress. The putative target genes of AP2/ERF transcription factors are highly diversified, suggesting that they play essential roles in various physiological responses in plants, including responses to biotic and abiotic stresses as well as developmental processes. Thus, this study of AP2/ERF genes and their functions provides valuable insight into how P. sativum responds to different environmental conditions, including cold and drought stresses.

Interfering small ubiquitin modifiers (SUMO) improves the thermotolerance of apple by facilitating the activity of MdDREB2A

Heat stress, which is caused by global warming, threatens crops yield and quality across the world. As a kind of post-translation modification, SUMOylation involves in plants heat stress response with a rapid and wide pattern. Here, we identified small ubiquitin modifiers (SUMO), which affect drought tolerance in apple, also participated in thermotolerance. Six isoforms of SUMOs located on six chromosomes in apple genome, and all the SUMOs were up-regulated in response to heat stress condition. The MdSUMO2 RNAi transgenic apple plants exhibited higher survival rate, lower ion leakage, higher catalase (CAT) activity, and Malondialdehyde (MDA) content under heat stress. MdDREB2A, the substrate of MdSUMO2 in apple, was accumulated in MdSUMO2 RNAi transgenic plants than the wild type GL-3 at the protein level in response to heat stress treatment. Further, the inhibited SUMOylation level of MdDREB2A in MdSUMO2 RNAi plants might repress its ubiquitination, too. The accumulated MdDREB2A in MdSUMO2 RNAi plants further induced heat-responsive genes expression to strengthen plants thermotolerance, including MdHSFA3, MdHSP26.5, MdHSP18.2, MdHSP70, MdCYP18-1 and MdTLP1. In summary, these findings illustrate that interfering small ubiquitin modifiers (SUMO) in apple improves plants thermotolerance, partly by facilitating the stability and activity of MdDREB2A.

Poly(ADP-ribose)-binding protein RCD1 is a plant PARylation reader regulated by Photoregulatory Protein Kinases

Poly(ADP-ribosyl)ation (PARylation) is a reversible post-translational protein modification that has profound regulatory functions in metabolism, development and immunity, and is conserved throughout the eukaryotic lineage. Contrary to metazoa, many components and mechanistic details of PARylation have remained unidentified in plants. Here we present the transcriptional co-regulator RADICAL-INDUCED CELL DEATH1 (RCD1) as a plant PAR-reader. RCD1 is a multidomain protein with intrinsically disordered regions (IDRs) separating its domains. We have reported earlier that RCD1 regulates plant development and stress-tolerance by interacting with numerous transcription factors (TFs) through its C-terminal RST domain. This study suggests that the N-terminal WWE and PARP-like domains, as well as the connecting IDR play an important regulatory role for RCD1 function. We show that RCD1 binds PAR in vitro via its WWE domain and that PAR-binding determines RCD1 localization to nuclear bodies (NBs) in vivo. Additionally, we found that RCD1 function and stability is controlled by Photoregulatory Protein Kinases (PPKs). PPKs localize with RCD1 in NBs and phosphorylate RCD1 at multiple sites affecting its stability. This work proposes a mechanism for negative transcriptional regulation in plants, in which RCD1 localizes to NBs, binds TFs with its RST domain and is degraded after phosphorylation by PPKs.

Clock-regulated coactivators selectively control gene expression in response to different temperature stress conditions in Arabidopsis

Plants respond to severe temperature changes by inducing the expression of numerous genes whose products enhance stress tolerance and responses. Dehydration-responsive element (DRE)-binding protein 1/C-repeat binding factor (DREB1/CBF) transcription factors act as master switches in cold-inducible gene expression. Since DREB1 genes are rapidly and strongly induced by cold stress, the elucidation of the molecular mechanisms of DREB1 expression is vital for the recognition of the initial responses to cold stress in plants. A previous study indicated that the circadian clock-related MYB-like transcription factors REVEILLE4/LHY-CCA1-Like1 (RVE4/LCL1) and RVE8/LCL5 directly activate DREB1 expression under cold stress conditions. These RVEs function in the regulation of circadian clock-related gene expression under normal temperature conditions. They also activate the expression of HSF-independent heat-inducible genes under high-temperature conditions. Thus, there are thought to be specific regulatory mechanisms whereby the target genes of these transcription factors are switched when temperature changes are sensed. We revealed that NIGHT LIGHT-INDUCIBLE AND CLOCK-REGULATED (LNK) proteins act as coactivators of RVEs in cold and heat stress responses in addition to regulating circadian-regulated genes at normal temperatures. We found that among the four Arabidopsis LNKs, LNK1 and LNK2 function under normal and high-temperature conditions, and LNK3 and LNK4 function under cold conditions. Thus, these LNK proteins play important roles in inducing specific genes under different temperature conditions. Furthermore, LNK3 and LNK4 are specifically phosphorylated under cold conditions, suggesting that phosphorylation is involved in their activation.

Ectopic expression of rice malate synthase in Arabidopsis revealed its roles in salt stress responses

Expression of rice malate synthase (OsMS), one of the two key genes in the glyoxylate cycle, is highly upregulated under salt stress. In this study, we aimed to investigate the role of OsMS in salt stress responses using the Arabidopsis T-DNA insertional mutant line of malate synthase (AtMS), an OsMS orthologous gene, for ectopic expression. Germination of the Atms mutant under salt stress was lower than that of Arabidopsis Col-0 wildtype (WT); furthermore, the two Atms mutant lines ectopically expressing OsMS reversed the salt-sensitive phenotype. Atms mutants salt-treated for 3 days exhibited higher electrolyte leakage, higher Na⁺/K⁺ ratio, lower expression of stress-responsive genes, and lower soluble sugar content than WT and the two OsMS-expressing Atms mutant lines. Consistently, Atms mutants salt-treated for 3 days followed by a 5-day recovery period displayed greater fresh-weight reduction. Notably, leaf greenness and chlorophyll and total carotenoid contents were higher in the Atms mutant lines than in the WT under stress. OsMS-expressing Atms mutants exhibited a change in pigment content closer to that of WT. During dark-induced senescence, an Atms mutant, Aticl, mutant (the other key gene in the glyoxylate cycle), and three double mutant lines of Atms and Aticl exhibited lower decreases in leaf greenness than the WT and OsMS-expressing Atms mutant lines. Furthermore, SAG12 expression levels in the Atms mutant, Aticl mutant, and three double mutant lines were lower than those in OsMS-expressing Atms mutant lines. Altogether, our data indicate that OsMS likely plays a key role in salt stress responses, possibly through the induction of leaf senescence.

Genome-Wide Association Studies of Salt Tolerance at the Seed Germination Stage and Yield-Related Traits in Brassica napus L

Salt stress severely affects crop growth and development and reduces the yield of Brassica napus. Exploring natural genetic variations for high salt tolerance in B. napus seedlings is an effective approach to improve productivity under salt stress. Using 10,658 high-quality single nucleotide polymorphic (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, genome-wide association studies (GWAS) were performed to investigate the genetic basis of salt tolerance and yield-related traits of B. napus. The results revealed that 77 and 497 SNPs were significantly associated with salt tolerance and yield-related traits, of which 40 and 58 SNPs were located in previously reported QTLs/SNPs, respectively. We identified nineteen candidate genes orthologous with Arabidopsis genes known to be associated with salt tolerance and seven potential candidates controlling both salt tolerance and yield. Our study provides a novel genetic resource for the breeding of high-yield cultivars resistant to salt stress.

Identification and Characterization of AP2/ERF Transcription Factors in Yellow Horn

The AP2/ERF gene family involves numerous plant processes, including growth, development, metabolism, and various plant stress responses. However, several studies have been conducted on the AP2/ERF gene family in yellow horn, a new type of oil woody crop and an essential oil crop in China. According to sequence alignment and phylogenetic analyses, one hundred and forty-five AP2/ERF genes were detected from the yellow horn genome. They were divided into four relatively conserved subfamilies, including 21 AP2 genes, 119 ERBP genes, 4 RAV genes, and 1 Soloist gene. Gene analysis of XsAP2/ERF TFs showed 87 XsAP2/ERF TFs lacked introns. There were 75 pairs of collinearity relationships between X. sorbifolium and Arabidopsis, indicating a close similarity. In addition, the expression patterns of XsAP2/ERF TFs under cold treatments confirmed that the XsAP2/ERF TFs play essential roles in abiotic stress response. The expression of eight XsAP2/ERF transcription factors was verified in different tissues and under various stress treatments using RT-qPCR. This study establishes a starting point for further research to explore the potential mechanisms of identifying candidate AP2/ERF TFs that could respond to the abiotic stress of yellow horn.

A Novel bHLH Transcription Factor PtrbHLH66 from Trifoliate Orange Positively Regulates Plant Drought Tolerance by Mediating Root Growth and ROS Scavenging

Drought limits citrus yield and fruit quality worldwide. The basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in plant response to drought stress. However, few bHLH TFs related to drought response have been functionally characterized in citrus. In this study, a bHLH family gene, named PtrbHLH66, was cloned from trifoliate orange. PtrbHLH66 contained a highly conserved bHLH domain and was clustered closely with bHLH66 homologs from other plant species. PtrbHLH66 was localized to the nucleus and had transcriptional activation activity. The expression of PtrbHLH66 was significantly induced by polyethylene glycol 6000 (PEG6000) and abscisic acid (ABA) treatments. Ectopic expression of PtrbHLH66 promoted the seed germination and root growth, increased the proline and ABA contents and the activities of antioxidant enzymes, but reduced the accumulation of malondialdehyde (MDA) and reactive oxygen species (ROS) under drought stress, resulting in enhanced drought tolerance of transgenic Arabidopsis. In contrast, silencing the PtrbHLH66 homolog in lemon plants showed the opposite effects. Furthermore, under drought stress, the transcript levels of 15 genes involved in ABA biosynthesis, proline biosynthesis, ROS scavenging and drought response were obviously upregulated in PtrbHLH66 ectopic-expressing Arabidopsis but downregulated in PtrbHLH66 homolog silencing lemon. Thus, our results suggested that PtrbHLH66 acted as a positive regulator of plant drought resistance by regulating root growth and ROS scavenging.

TaFDL2-1A confers drought stress tolerance by promoting ABA biosynthesis, ABA responses, and ROS scavenging in transgenic wheat

Plants have developed various protective mechanisms to survive drought stress. Previously, it was shown that a wheat bZIP transcription factor gene TaFD-Like2-1A (TaFDL2-1A) can confer drought tolerance in Arabidopsis. However, the biological functions related to drought stress tolerance of TaFDL2-1A in wheat (Triticum aestivum L.) remain unclear. In the present study, overexpression of TaFDL2-1A in the wheat cultivar Fielder improved drought resistance and conferred abscisic acid (ABA) hypersensitivity. Further analysis showed that overexpression of TaFDL2-1A increased the hypersensitivity of stomata to drought stress and endogenous ABA content under drought conditions. Genetic analysis and transcriptional regulation analysis indicated that TaFDL2-1A binds directly to the promoter fragments of TaRAB21s and TaNCED2s via ACGT core cis-elements, thereby activating their expression, leading to enhanced ABA responses and endogenous ABA accumulation. In addition, our results demonstrate that overexpression of TaFDL2-1A results in higher SOD and GPX activities in wheat under drought conditions by promoting the expression of TaSOD1 and TaGPx1-D, indicating enhanced reactive oxygen species (ROS) scavenging. These results imply that TaFDL2-1A positively regulates ABA biosynthesis, ABA responses, and ROS scavenging to improve drought stress tolerance in transgenic wheat. Our findings improve our understanding of the mechanisms that allow the wheat bZIP transcription factor to improve drought resistance and provide a useful reference gene for breeding programs to enhance drought resistance.

Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.)

Background

RING (Really Interesting New Gene) zinc finger (RING-zf) proteins belong to an important subclass of zinc fingers superfamily, which play versatile roles during various developmental stages and in abiotic stress responses. Based on the conserved cysteine and histidine residues, the RING-zf domains are classified into RING-HC (C3HC4), RING-H2 (C3H2C3), RING-v, RING-D, RING-S/T, RING-G, and RING-C2. However, little is known about the function of the RING-zfs of wheat.

Results

In this study, 129 (93.5%) of 138 members were found in nucleus, indicating TaRING-zf were primarily engaged in the degradation of transcription factors and other nuclear-localized proteins. 138 TaRING-zf domains can be divided into four canonical or modified types (RING-H2, RING-HC, RING-D, and RING-M). The RING-M was newly identified in T. aestivum, and might represent the intermediate other states between RING-zf domain and other modified domains. The consensus sequence of the RING-M domain can be described as M-X₂-R-X₁₄-Cys-X₁-H-X₂-Cys-X₂-Cys-X₁₀-Cys-X₂-Cys. Further interspecies collinearity analyses showed that TaRING-zfs were more closely related to the genes in Poaceae. According to the public transcriptome data, most of the TaRING-zfs were expressed at different 15 stages of plant growth, development, and some of them exhibited specific responses to drought/heat stress. Moreover, 4 RING-HC (TraesCS2A02G526800.1, TraesCS4A02G290600.1, TraesCS4B02G023600.1 and TraesCS4D02G021200.1) and 2 RING-H2 (TraesCS3A02G288900.1 and TraesCS4A02G174600.1) were significantly expressed at different development stages and under drought stress. These findings provide valuable reference data for further study of their physiological functions in wheat varieties.

Conclusions

Taken together, the characterization and classifications of the TaRING-zf family were extensively studied and some new features about it were revealed. This study could provide some valuable targets for further studies on their functions in growth and development, and abiotic stress responses in wheat.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08905-x.

Transcript profiling of Polycomb gene family in Oryza sativa indicates their abiotic stress-specific response

The precise regulation of gene expression is required for the determination of cell fate, differentiation, and developmental programs in eukaryotes. The Polycomb Group (PcG) genes are the key transcriptional regulators that constitute the repressive system, with two major protein complexes, Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2). Previous studies have demonstrated the significance of these proteins in regulation of normal growth and development processes. However, the role of PcG in adaptation of crops to abiotic stress is still not well understood. The present study aimed to a comprehensive genome-wide identification of the PcG gene family in one of the economically important staple crops, Oryza sativa. Here, a total of 14 PcG genes have been identified, which were distributed over eight chromosomes. Protein structure analysis revealed that both the complexes have distinct domain and motifs that are conserved within the complexes. In silico promoter analysis showed that PcG gene promoters have abundance of abiotic stress-responsive elements. RNA-seq based expression analysis revealed that PcG genes are differentially expressed in different tissues and responded variably in different environmental stress. Validation of gene expression by qRT-PCR showed that most of the genes were upregulated at 1-h time point in shoot tissue and at 24-h time point in root tissue under the drought and salinity stress conditions. These findings provide important and extensive information on the PcG family of O. sativa, which will pave the path for understanding their role in stress signaling in plants.

Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum

The zinc finger protein (ZFP) family is one of plants’ most diverse family of transcription factors. These proteins with finger-like structural domains have been shown to play a critical role in plant responses to abiotic stresses such as drought. This study aimed to systematically characterize Triticum aestivum ZFPs (TaZFPs) and understand their roles under drought stress. A total of 9 TaC2H2, 38 TaC3HC4, 79 TaCCCH, and 143 TaPHD were identified, which were divided into 4, 7, 12, and 14 distinct subgroups based on their phylogenetic relationships, respectively. Segmental duplication dominated the evolution of four subfamilies and made important contributions to the large-scale amplification of gene families. Syntenic relationships, gene duplications, and Ka/Ks result consistently indicate a potential strong purifying selection on TaZFPs. Additionally, TaZFPs have various abiotic stress-associated cis-acting regulatory elements and have tissue-specific expression patterns showing different responses to drought and heat stress. Therefore, these genes may play multiple functions in plant growth and stress resistance responses. This is the first comprehensive genome-wide analysis of ZFP gene families in T. aestivum to elucidate the basis of their function and resistance mechanisms, providing a reference for precise manipulation of genetic engineering for drought resistance in T. aestivum.

VAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC

Polycomb (PcG) silencing is crucial for development, but how targets are specified remains incompletely understood. The cold-induced Polycomb Repressive Complex 2 (PRC2) silencing of Arabidopsis thaliana FLOWERING LOCUS C (FLC) provides an excellent system to elucidate PcG regulation. Association of the DNA binding protein VAL1 to FLC PcG nucleation regionis an important step. VAL1 co-immunoprecipitates APOPTOSIS AND SPLICING ASSOCIATED PROTEIN (ASAP) complex and PRC1. Here, we show that ASAP and PRC1 are necessary for co-transcriptional repression and chromatin regulation at FLC. ASAP mutants affect FLC transcription in warm conditions, but the rate of FLC silencing in the cold is unaffected. PRC1-mediated H2Aub accumulation increases at the FLC nucleation region during cold, but unlike the PRC2-delivered H3K27me3, does not spread across the locus. H2Aub thus involved in the transition to epigenetic silencing at FLC, facilitating H3K27me3 accumulation and long-term epigenetic memory. Overall, our work highlights the importance of VAL1 as an assembly platform co-ordinating activities necessary for epigenetic silencing at FLC.

Current perspectives of ubiquitination and SUMOylation in abiotic stress tolerance in plants

Post-translational modification (PTM) is a critical and rapid mechanism to regulate all the major cellular processes through the modification of diverse protein substrates. Substrate-specific covalent attachment of ubiquitin and Small Ubiquitin-Like Modifier (SUMO) with the target proteins, known as ubiquitination and SUMOylation, respectively, are crucial PTMs that regulate almost every process in the cell by modulating the stability and fidelity of the proteins. Ubiquitination and SUMOylation play a very significant role to provide tolerance to the plants in adverse environmental conditions by activating/deactivating the pre-existing proteins to a great extent. We reviewed the importance of ubiquitination and SUMOylation in plants, implicating its prospects in various abiotic stress regulations. An exhaustive study of molecular mechanisms of ubiquitination and SUMOylation of plant proteins and their role will contribute to the understanding of physiology underlying mitigation of the abiotic stresses and survival in plants. It will be helpful to strategize the improvement of crops for abiotic stress tolerance.

Key factors for differential drought tolerance in two contrasting wild materials of Artemisia wellbyi identified using comparative transcriptomics

BACKGROUND

Drought is a significant condition that restricts vegetation growth on the Tibetan Plateau. Artemisia wellbyi is a unique semi-shrub-like herb in the family Compositae, which distributed in northern and northwest of Tibetan Plateau. It is a dominant species in the community that can well adapt to virous environment stress, such as drought and low temperature. Therefore, A. wellbyi. has a potential ecological value for soil and water conservation of drought areas. Understanding the molecular mechanisms of A. wellbyi. that defense drought stress can acquire the key genes for drought resistance breeding of A. wellbyi. and provide a theoretical basis for vegetation restoration of desertification area. However, they remain unclear. Thus, our study compared the transcriptomic characteristics of drought-tolerant "11" and drought-sensitive "6" material of A. wellbyi under drought stress.

RESULTS

A total of 4875 upregulated and 4381 downregulated differentially expressed genes (DEGs) were induced by drought in the tolerant material; however, only 1931 upregulated and 4174 downregulated DEGs were induced by drought in the sensitive material. The photosynthesis and transcriptional regulation differed significantly with respect to the DEGs number and expression level. We found that CDPKs (calmodulin-like domain protein kinases), SOS3 (salt overly sensitive3), MAPKs (mitogen-activated protein kinase cascades), RLKs (receptor like kinase), and LRR-RLKs (repeat leucine-rich receptor kinase) were firstly involved in response to drought stress in drought tolerant A. wellbyi. Positive regulation of genes associated with the metabolism of ABA (abscisic acid), ET (ethylene), and IAA (indole acetic acid) could play a crucial role in the interaction with other transcriptional regulatory factors, such as MYBs (v-myb avian myeloblastosis viral oncogene homolog), AP2/EREBPs (APETALA2/ethylene-responsive element binding protein family), WRKYs, and bHLHs (basic helix-loop-helix family members) and receptor kinases, and regulate downstream genes for defense against drought stress. In addition, HSP70 (heat shock protein70) and MYB73 were considered as the hub genes because of their strong association with other DEGs.

CONCLUSIONS

Positive transcriptional regulation and negative regulation of photosynthesis could be associated with better growth performance under drought stress in the drought-tolerant material. In addition, the degradation of sucrose and starch in the tolerant A. wellbyi to alleviate osmotic stress and balance excess ROS. These results highlight the candidate genes that are involved in enhancing the performance of drought-tolerant A. wellbyi and provide a theoretical basis for improving the performance of drought-resistant A. wellbyi.

Functions and mechanisms of the Ubc13-UEV complex and lysine 63-linked polyubiquitination in plants

Ubiquitination is one of the best-known post-translational modifications in eukaryotes, in which different linkage types of polyubiquitination result in different outputs of the target proteins. Distinct from the well-characterized K48-linked polyubiquitination that usually serves as a signal for degradation of the target protein, K63-linked polyubiquitination often requires a unique E2 heterodimer Ubc13-UEV and alters the target protein activity instead of marking it for degradation. This review focuses on recent advances on the roles of Ubc13-UEV-mediated K63-linked polyubiquitination in plant growth, development, and response to environmental stresses.

E3 ligase AtAIRP5/GARU regulates drought stress response by stimulating SERINE CARBOXYPEPTIDASE-LIKE1 turnover

Ubiquitination is a major mechanism of eukaryotic posttranslational protein turnover that has been implicated in abscisic acid (ABA)-mediated drought stress response. Here, we isolated T-DNA insertion mutant lines in which ABA-insensitive RING protein 5 (AtAIRP5) was suppressed, resulting in hyposensitive ABA-mediated germination compared to wild-type Arabidopsis (Arabidopsis thaliana) plants. A homology search revealed that AtAIRP5 is identical to gibberellin (GA) receptor RING E3 ubiquitin (Ub) ligase (GARU), which downregulates GA signaling by degrading the GA receptor GID1, and thus AtAIRP5 was renamed AtAIRP5/GARU. The atairp5/garu knockout progeny were impaired in ABA-dependent stomatal closure and were markedly more susceptible to drought stress than wild-type plants, indicating a positive role for AtAIRP5/GARU in the ABA-mediated drought stress response. Yeast two-hybrid, pull-down, target ubiquitination, and in vitro and in planta degradation assays identified serine carboxypeptidase-like1 (AtSCPL1), which belongs to the clade 1A AtSCPL family, as a ubiquitinated target protein of AtAIRP5/GARU. atscpl1 single and atairp5/garu-1 atscpl1-2 double mutant plants were more tolerant to drought stress than wild-type plants in an ABA-dependent manner, suggesting that AtSCPL1 is genetically downstream of AtAIRP5/GARU. After drought treatment, the endogenous ABA levels in atscpl1 and atairp5/garu-1 atscpl1-2 mutant leaves were higher than those in wild-type and atairp5/garu leaves. Overall, our results suggest that AtAIRP5/GARU RING E3 Ub ligase functions as a positive regulator of the ABA-mediated drought response by promoting the degradation of AtSCPL1.

Dynamic modeling of ABA-dependent expression of the Arabidopsis RD29A gene

The abscisic acid (ABA) signaling pathway is the key defense mechanism against drought stress in plants. In the pathway, signal transduction among four core proteins, pyrabactin resistance (PYR), protein phosphatase 2C (PP2C), sucrose-non-fermenting-1-related protein kinase 2 (SnRK2), and ABRE binding factor (ABF) leads to altered gene expression kinetics that is driven by an ABA-responsive element (ABRE). A most recent and comprehensive study provided data suggesting that ABA alters the expression kinetics in over 6,500 genes through the ABF-ABRE associations in Arabidopsis. Of these genes, termed ABA gene regulatory network (GRN), over 50% contain a single ABRE within 4 kb of the gene body, despite previous findings suggesting that a single copy of ABRE is not sufficient to drive the gene expression. To understand the expression system of the ABA GRN by the single ABRE, a dynamic model of the gene expression for the desiccation 29A (RD29A) gene was constructed with ordinary differential equations. Parameter values of molecular-molecular interactions and enzymatic reactions in the model were implemented from the data obtained by previously conducted in vitro experiments. On the other hand, parameter values of gene expression and translation were determined by comparing the kinetics of gene expression in the model to the expression kinetics of RD29A in real plants. The optimized model recapitulated the trend of gene expression kinetics of RD29A in ABA dose-response that were previously investigated. Further analysis of the model suggested that a single ABRE controls the time scale and dynamic range of the ABA-dependent gene expression through the PP2C feedback regulation even though an additional cis-element is required to drive the expression. The model construed in this study underpins the importance of a single ABRE in the ABA GRN.

Effects of the Rhizosphere Fungus Cunninghamella bertholletiae on the Solanum lycopersicum Response to Diverse Abiotic Stresses

This study examined the efficiency of fungal strain (Cunninghamella bertholletiae) isolated from the rhizosphere of Solanum lycopersicum to reduce symptoms of salinity, drought and heavy metal stresses in tomato plants. In vitro evaluation of C. bertholletiae demonstrated its ability to produce indole-3-Acetic Acid (IAA), ammonia and tolerate varied abiotic stresses on solid media. Tomato plants at 33 days’ old, inoculated with or without C. bertholletiae, were treated with 1.5% sodium chloride, 25% polyethylene glycol, 3 mM cadmium and 3 mM lead for 10 days, and the impact of C. bertholletiae on plant performance was investigated. Inoculation with C. bertholletiae enhanced plant biomass and growth attributes in stressed plants. In addition, C. bertholletiae modulated the physiochemical apparatus of stressed plants by raising chlorophyll, carotenoid, glucose, fructose, and sucrose contents, and reducing hydrogen peroxide, protein, lipid metabolism, amino acid, antioxidant activities, and abscisic acid. Gene expression analysis showed enhanced expression of SlCDF3 and SlICS genes and reduced expression of SlACCase, SlAOS, SlGRAS6, SlRBOHD, SlRING1, SlTAF1, and SlZH13 genes following C. bertholletiae application. In conclusion, our study supports the potential of C. bertholletiae as a biofertilizer to reduce plant damage, improve crop endurance and remediation under stress conditions.

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

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

Regulatory network established by transcription factors transmits drought stress signals in plant

Plants are sessile organisms that evolve with a flexible signal transduction system in order to rapidly respond to environmental changes. Drought, a common abiotic stress, affects multiple plant developmental processes especially growth. In response to drought stress, an intricate hierarchical regulatory network is established in plant to survive from the extreme environment. The transcriptional regulation carried out by transcription factors (TFs) is the most important step for the establishment of the network. In this review, we summarized almost all the TFs that have been reported to participate in drought tolerance (DT) in plant. Totally 466 TFs from 86 plant species that mostly belong to 11 families are collected here. This demonstrates that TFs in these 11 families are the main transcriptional regulators of plant DT. The regulatory network is built by direct protein-protein interaction or mutual regulation of TFs. TFs receive upstream signals possibly via post-transcriptional regulation and output signals to downstream targets via direct binding to their promoters to regulate gene expression.

Wheat E3 ubiquitin ligase TaGW2-6A degrades TaAGPS to affect seed size

TaGW2 has been identified as a key determinant of the grain weight in wheat (Triticum aestivum L.). In our previous study, we found that the grain size differs in Chinese Spring (CS) and its TaGW2-6A allelic variant (NIL31). In addition, the expression of the key starch biosynthesis enzyme gene TaAGPS differs significantly in the two materials. However, the underlying molecular mechanism associated with the action of TaGW2-6A has not been reported. In the present study, we found that TaGW2-6A-CS interacted with TaAGPS, whereas TaGW2-6A-NIL31 did not interact with it in vitro and in vivo. Furthermore, we found that the C-terminal LXLX domain (376-424 aa) of TaGW2-6A recognized TaAGPS. However, the TaGW2-6A allelic variant lacked this key interaction region due to premature translation termination. We also found that TaGW2-6A-CS can ubiquitinate TaAGPS and degrade it via the 26 S proteasome pathway. In addition, our analysis of the activity of ADP-glucose pyrophosphorylase (AGPase) indicated that the AGPase level in the endosperm cells was lower in CS than NIL31. Cytological observations demonstrated that the average number of starch granules and the average area of starch granules in endosperm cells were lower in CS than NIL31. The overexpression of TaAGPS positively regulated the seed size in transgenic Arabidopsis. Our findings provide novel insights into the molecular mechanism that allows TaGW2-6A-TaAGPS to regulate seed size via the starch synthesis pathway.