CBF4/DREB1D represses XERICO to attenuate ABA, osmotic and drought stress responses in Arabidopsis

Genome-wide identification of the AP2/ERF gene family from Limonium bicolor and functional characterization of LbAP2/ERF32 under salt stress

AP2/ERF transcription factors (TFs) play important roles in plant growth and development, plant morphogenesis and response to environmental stresses. However, their biological roles in recretohalophytes are still not fully revealed. Limonium bicolor L. is a typical recretohalophyte, which secretes excessive salt ions through the salt glands on the epidermis. Here, 64 LbAP2/ERF genes were identified in L. bicolor genome, which were unevenly distributed on the eight chromosomes. Cis-elements related to growth and development, stress response and phytohormone response are distributed in multiple LbAP2/ERF promoters. Expression analysis indicated that LbAP2/ERF genes responsed to NaCl, PEG and ABA. And the salt gland density, salt secretion of leaves and overall salt tolerance of LbAP2/ERF32 silenced lines were significantly reduced. In agreement, the genes related to salt gland development and ion transport were significantly changed in LbAP2/ERF32-silenced lines. Our findings provided fundamental information on the structure and evolutionary relationship of LbAP2/ERF gene family in salt gland development and salt secretion of L. bicolor and gave theoretical guideline for further functional study of LbAP2/ERF genes in response to abiotic stress.

Multifaceted insights into the environmental adaptability of Arnebia guttata under drought stress

Introduction

Global warming has led to increased environmental stresses on plants, notably drought. This affects plant distribution and species adaptability, with some medicinal plants showing enhanced drought tolerance and increased medicinal components. In this pioneering study, we delve into the intricate tapestry of Arnebia guttata, a medicinal plant renowned for its resilience in arid environments. By fusing a rich historical narrative with cutting-edge analytical methodologies, this research endeavors to demystify the plant's intricate response to drought stress, illuminating its profound implications for medicinal valorization.

Methods

The methodology includes a comprehensive textual research and resource investigation of A. guttata, regionalization studies, field sample distribution analysis, transcriptome and metabolome profiling, rhizosphere soil microbiome analysis, and drought stress experiments. Advanced computational tools like ArcGIS, MaxEnt, and various bioinformatics software were utilized for data analysis and modeling.

Results

The study identified significant genetic variations among A. guttata samples from different regions, correlating with environmental factors, particularly precipitation during the warmest quarter (BIO18). Metabolomic analysis revealed marked differences in metabolite profiles, including shikonin content, which is crucial for the plant's medicinal properties. Soil microbial community analysis showed variations that could impact plant metabolism and stress response. Drought stress experiments demonstrated A. guttata's resilience and its ability to modulate metabolic pathways to enhance drought tolerance.

Discussion

The findings underscore the complex interplay between genetic makeup, environmental factors, and microbial communities in shaping A. guttata's adaptability and medicinal value. The study provides insights into how drought stress influences the synthesis of active compounds and suggests that moderate stress could enhance the plant's medicinal properties. Predictive modeling indicates future suitable growth areas for A. guttata, aiding in resource management and conservation efforts. The research contributes to the sustainable development of medicinal resources and offers strategies for improving the cultivation of A. guttata.

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.

The chromatin remodeller MdRAD5B enhances drought tolerance by coupling MdLHP1-mediated H3K27me3 in apple

RAD5B belongs to the Rad5/16-like group of the SNF2 family, which often functions in chromatin remodelling. However, whether RAD5B is involved in chromatin remodelling, histone modification, and drought stress tolerance is largely unclear. We identified a drought-inducible chromatin remodeler, MdRAD5B, which positively regulates apple drought tolerance. Transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) analysis showed that MdRAD5B affects the expression of 466 drought-responsive genes through its chromatin remodelling function in response to drought stress. In addition, MdRAD5B interacts with and degrades MdLHP1, a crucial regulator of histone H3 trimethylation at K27 (H3K27me3), through the ubiquitin-independent 20S proteasome. Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis revealed that MdRAD5B modulates the H3K27me3 deposition of 615 genes in response to drought stress. Genetic interaction analysis showed that MdRAD5B mediates the H3K27me3 deposition of drought-responsive genes through MdLHP1, which causes their expression changes under drought stress. Our results unravelled a dual function of MdRAD5B in gene expression modulation in apple in response to drought, that is, via the regulation of chromatin remodelling and H3K27me3.

ABA guides stomatal proliferation and patterning through the EPF-SPCH signaling pathway in Arabidopsis thaliana

Adaptation to dehydration stress requires plants to coordinate environmental and endogenous signals to inhibit stomatal proliferation and modulate their patterning. The stress hormone abscisic acid (ABA) induces stomatal closure and restricts stomatal lineage to promote stress tolerance. Here, we report that mutants with reduced ABA levels, xer-1, xer-2 and aba2-2, developed stomatal clusters. Similarly, the ABA signaling mutant snrk2.2/2.3/2.6, which lacks core ABA signaling kinases, also displayed stomatal clusters. Exposure to ABA or inhibition of ABA catabolism rescued the increased stomatal density and spacing defects observed in xer and aba2-2, suggesting that basal ABA is required for correct stomatal density and spacing. xer-1 and aba2-2 displayed reduced expression of EPF1 and EPF2, and enhanced expression of SPCH and MUTE. Furthermore, ABA suppressed elevated SPCH and MUTE expression in epf2-1 and epf1-1, and partially rescued epf2-1 stomatal index and epf1-1 clustering defects. Genetic analysis demonstrated that XER acts upstream of the EPF2-SPCH pathway to suppress stomatal proliferation, and in parallel with EPF1 to ensure correct stomatal spacing. These results show that basal ABA and functional ABA signaling are required to fine-tune stomatal density and patterning.

Transcriptional reprogramming during recovery from drought stress in Eucalyptus grandis

The importance of drought as a constraint to agriculture and forestry is increasing with climate change. Genetic improvement of plants' resilience is one of the mitigation strategies to curb this threat. Although recovery from drought stress is important to long-term drought adaptation and has been considered as an indicator of dehydration tolerance in annual crops, this has not been well explored in forest trees. Thus, we aimed to investigate the physiological and transcriptional changes during drought stress and rewatering in Eucalyptus grandis W. Hill ex Maiden. We set up a greenhouse experiment where we imposed drought stress on 2-year-old seedlings and rewatered the recovery group after 17 days of drought. Our measurement of leaf stomatal conductance (gs) showed that, while gs was reduced by drought stress, it fully recovered after 5 days of rewatering. The RNA-seq analysis from stem samples revealed that genes related to known stress responses such as phytohormone and reactive oxygen species signaling were upregulated, while genes involved in metabolism and growth were downregulated due to drought stress. We observed reprogramming of signal transduction pathways and metabolic processes at 1 day of rewatering, indicating a quick response to rewatering. Our results suggest that recovery from drought stress may entail alterations in the jasmonic acid, salicylic acid, ethylene and brassinosteroid signaling pathways. Using co-expression network analysis, we identified hub genes, including the putative orthologs of ABI1, ABF2, ABF3, HAI2, BAM1, GolS2 and SIP1 during drought and CAT2, G6PD1, ADG1 and FD-1 during recovery. Taken together, by highlighting the molecular processes and identifying key genes, this study gives an overview of the mechanisms underlying the response of E. grandis to drought stress and recovery that trees may face repeatedly throughout their long life cycle. This provides a useful reference to the identification and further investigation of signaling pathways and target genes for future tree improvement.

Comparative transcriptome analysis reveals the function of SlPRE2 in multiple phytohormones biosynthesis, signal transduction and stomatal development in tomato

KEY MESSAGE

Transcriptomic, physiological, and qRT-PCR analysis revealed the potential mechanism by which SlPRE2 regulates plant growth and stomatal size via multiple phytohormone pathways in tomato. Paclobutrazol resistance proteins (PREs) are atypical members of the basic/helix-loop-helix (bHLH) transcription factor family that regulate plant morphology, cell size, pigment metabolism and abiotic stress in response to different phytohormones. However, little is known about the network regulatory mechanisms of PREs in plant growth and development in tomato. In this study, the function and mechanism of SlPRE2 in tomato plant growth and development were investigated. The quantitative RT-PCR results showed that the expression of SlPRE2 was regulated by multiple phytohormones and abiotic stresses. It showed light-repressed expression during the photoperiod. The RNA-seq results revealed that SlPRE2 regulated many genes involved in photosynthesis, chlorophyll metabolism, phytohormone metabolism and signaling, and carbohydrate metabolism, suggesting the role of SlPRE2 in gibberellin, brassinosteroid, auxin, cytokinin, abscisic acid and salicylic acid regulated plant development processes. Moreover, SlPRE2 overexpression plants showed widely opened stomata in young leaves, and four genes involved in stomatal development showed altered expression. Overall, the results demonstrated the mechanism by which SlPRE2 regulates phytohormone and stress responses and revealed the function of SlPRE2 in stomatal development in tomato. These findings provide useful clues for understanding the molecular mechanisms of SlPRE2-regulated plant growth and development in tomato.

The RING-H2 gene LdXERICO plays a negative role in dormancy release regulated by low temperature in Lilium davidii var. unicolor

Dormancy regulation is the basis of the sustainable development of the lily industry. Therefore, basic research on lily dormancy is crucial for innovation in lily cultivation and breeding. Previous studies revealed that dormancy release largely depends on abscisic acid (ABA) degradation. However, the key genes and potential regulatory network remain unclear. We used exogenous ABA and ABA inhibitors to elucidate the effect of ABA on lily dormancy. Based on the results of weighted gene coexpression network analysis (WGCNA), the hub gene LdXERICO was identified in modules highly related to endogenous ABA, and a large number of coexpressed genes were identified. LdXERICO was induced by exogenous ABA and expressed at higher levels in tissues with vigorous physiological activity. Silencing LdXERICO increased the low-temperature sensitivity of bulblets and accelerated bulblet sprouting. LdXERICO rescued the ABA insensitivity of xerico mutants during seed germination in Arabidopsis, suggesting that it promotes seed dormancy and supporting overexpression studies on lily bulblets. The significant increase in ABA levels in transgenic Arabidopsis expressing LdXERICO indicated that LdXERICO played a role by promoting ABA synthesis. We generated three transgenic lines by overexpressing LdICE1 in Arabidopsis thaliana and showed that, in contrast to LdXERICO, LdICE1 positively regulated dormancy release. Finally, qRT-PCR confirmed that LdXERICO was epistatic to LdICE1 for dormancy release. We propose that LdXERICO, an essential gene in dormancy regulation through the ABA-related pathway, has a complex regulatory network involving temperature signals. This study provides a theoretical basis for further exploring the mechanism of bulb dormancy release.

Cold-Induced Nuclear Import of CBF4 Regulates Freezing Tolerance

C-repeat binding factors (CBFs) are crucial transcriptional activators in plant responses to low temperature. CBF4 differs in its slower, but more persistent regulation and its role in cold acclimation. Cold acclimation has accentuated relevance for tolerance to late spring frosts as they have become progressively more common, as a consequence of blurred seasonality in the context of global climate change. In the current study, we explore the functions of CBF4 from grapevine, VvCBF4. Overexpression of VvCBF4 fused to GFP in tobacco BY-2 cells confers cold tolerance. Furthermore, this protein shuttles from the cytoplasm to the nucleus in response to cold stress, associated with an accumulation of transcripts for other CBFs and the cold responsive gene, ERD10d. This response differs for chilling as compared to freezing and is regulated differently by upstream signalling involving oxidative burst, proteasome activity and jasmonate synthesis. The difference between chilling and freezing is also seen in the regulation of the CBF4 transcript in leaves from different grapevines differing in their cold tolerance. Therefore, we propose the quality of cold stress is transduced by different upstream signals regulating nuclear import and, thus, the transcriptional activation of grapevine CBF4.

Specific CBF transcription factors and cold-responsive genes fine-tune the early triggering response after acquisition of cold priming and memory

Plants need to adapt to fluctuating temperatures throughout their lifetime. Previous research showed that Arabidopsis memorizes a first cold stress (priming) and improves its primed freezing tolerance further when subjected to a second similar stress after a lag phase. This study investigates primary metabolomic and transcriptomic changes during early cold priming or triggering after 3 days at 4°C interrupted by a memory phase. DREB1 family transcription factors DREB1C/CBF2, DREB1D/CBF4, DREB1E/DDF2, and DREB1F/DDF1 were strongly significantly induced throughout the entire triggering. During triggering, genes encoding Late Embryogenesis Abundant (LEA), antifreeze proteins or detoxifiers of reactive oxygen species (ROS) were higher expressed compared with priming. Examples of early triggering responders were xyloglucan endotransglucosylase/hydrolase genes encoding proteins involved in cell wall remodeling, while late responders were identified to act in fine-tuning the stress response and developmental regulation. Induction of non-typical members of the DREB subfamily of ERF/AP2 transcription factors, the relatively small number of induced CBF regulon genes and a slower accumulation of selected cold stress associated metabolites indicate that a cold triggering stimulus might be sensed as milder stress in plants compared with priming. Further, strong induction of CBF4 throughout triggering suggests a unique function of this gene for the response to alternating temperatures.

Dehydration-Responsive Element Binding Protein 1C, 1E, and 1G Promote Stress Tolerance to Chilling, Heat, Drought, and Salt in Rice

The dehydration-responsive element binding protein 1 (DREB1)/C-repeat-binding factor (CBF) genes are key regulators of cold acclimation and freezing tolerance in the chilling tolerant Arabidopsis thaliana. Here, we investigated the function of three members of the 10 rice DREB1 genes, OsDREB1C, E, and G, in the chilling sensitive rice plants. Their loss of function (LOF) mutants were each more chilling susceptible compared to the wild type, and the LOF mutants of all three genes, dreb1ceg, were more chilling susceptible than any of the single mutants. Strikingly, these mutants were capable of cold acclimation, indicating that these rice DREB1 genes are important for basal chilling tolerance but not cold acclimation. Transcriptome and physiology analyses suggest that the OsDREB1C/E/G genes are involved in reactive oxygen species (ROS) scavenging and cell death regulation under chilling. Furthermore, these three rice DREB1 genes are found to promote tolerance to other abiotic stresses: the OsDREB1C/E/G genes are positive regulators of heat tolerance, OsDREB1C and OsDREB1G are positive regulators of salt tolerance, and OsDREB1G is a positive regulator of drought tolerance. These findings expand our knowledge of the roles of DREB1 proteins in plants, enhance our mechanistic understanding of abiotic stress tolerance and will facilitate the generation of stress-tolerant crop plants.