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

The transcriptional regulation of a putative hemicellulose gene, PtrPARVUS2 in poplar

The plant cell wall serves as a critical interface between the plant and its environment, offering protection against various stresses and contributing to biomass production. Hemicellulose is one of the major components of the cell wall, and understanding the transcriptional regulation of its production is essential to fully understanding cell wall formation. This study explores the regulatory mechanisms underlying one of the genes involved in hemicellulose biosynthesis, PtrPARVUS2. Six transcription factors (TFs) were identified from a xylem-biased library to negatively regulate PtrPARVUS2 expression. These TFs, belonging to diverse TF families, were confirmed to bind to specific cis-elements in the PtrPARVUS2 promoter region, as validated by Yeast One-Hybrid (Y1H) assays, transient expression analysis, and Chromatin Immunoprecipitation sequencing (ChIP-seq) assays. Furthermore, motif analysis identified putative cis-regulatory elements bound by these TFs, shedding light on the transcriptional regulation of SCW biosynthesis genes. Notably, several TFs targeted genes encoding uridine diphosphate glycosyltransferases (UGTs), crucial enzymes involved in hemicellulose glycosylation. Phylogenetic analysis of UGTs regulated by these TFs highlighted their diverse roles in modulating hemicellulose synthesis. Overall, this study identifies a set of TFs that regulate PARVUS2 in poplar, providing insights into the intricate coordination of TFs and PtrPARVUS2 in SCW formation. Understanding these regulatory mechanisms enhances our ability to engineer plant biomass for tailored applications, including biofuel production and bioproduct development.

Modulation of the wheat transcriptome by TaZFP13D under well-watered and drought conditions

Maintaining global food security in the context of climate changes will be an important challenge in the next century. Improving abiotic stress tolerance of major crops such as wheat can contribute to this goal. This can be achieved by the identification of the genes involved and their use to develop tools for breeding programs aiming to generate better adapted cultivars. Recently, we identified the wheat TaZFP13D gene encoding Zinc Finger Protein 13D as a new gene improving water-stress tolerance. The current work analyzes the TaZFP13D-dependent transcriptome modifications that occur in well-watered and dehydration conditions to better understand its function during normal growth and during drought. Plants that overexpress TaZFP13D have a higher biomass under well-watered conditions, indicating a positive effect of the protein on growth. Survival rate and stress recovery after a severe drought stress are improved compared to wild-type plants. The latter is likely due the higher activity of key antioxidant enzymes and concomitant reduction of drought-induced oxidative damage. Conversely, down-regulation of TaZFP13D decreases drought tolerance and protection against drought-induced oxidative damage. RNA-Seq transcriptome analysis identified many genes regulated by TaZFP13D that are known to improve drought tolerance. The analysis also revealed several genes involved in the photosynthetic electron transfer chain known to improve photosynthetic efficiency and chloroplast protection against drought-induced ROS damage. This study highlights the important role of TaZFP13D in wheat drought tolerance, contributes to unravel the complex regulation governed by TaZFPs, and suggests that it could be a promising marker to select wheat cultivars with higher drought tolerance.

Transcriptomic and metabolomic profiling reveals the drought tolerance mechanism of Illicium difengpi (Schisandraceae)

Illicium difengpi (Schisandraceae), an endangered medicinal plant endemic to karst areas, is highly tolerant to drought and thus can be used as an ideal material for investigating adaptive mechanism to drought stress. The understanding of the drought tolerance of I. difengpi, especially at the molecular level, is lacking. In the present study, we aimed to clarify the molecular mechanism underlying drought tolerance in endemic I. difengpi plant in karst regions. The response characteristics of transcripts and changes in metabolite abundance of I. difengpi subjected to drought and rehydration were analyzed, the genes and key metabolites responsive to drought and rehydration were screened, and some important biosynthetic and secondary metabolic pathways were identified. A total of 231,784 genes and 632 metabolites were obtained from transcriptome and metabolome analyses, and most of the physiological metabolism in drought-treated I. difengpi plants recovered after rehydration. There were more upregulated genes than downregulated genes under drought and rehydration treatments, and rehydration treatment induced stable expression of 65.25% of genes, indicating that rehydration alleviated drought stress to some extent. Drought and rehydration treatment generated flavonoids, phenolic acids, flavonols, amino acids and their derivatives, as well as metabolites such as saccharides and alcohols in the leaves of I. difengpi plants, which alleviated the injury caused by excessive reactive oxygen species. The integration of transcriptome and metabolome analyses showed that, under drought stress, I. difengpi increased glutathione, flavonoids, polyamines, soluble sugars and amino acids, contributing to cell osmotic potential and antioxidant activity. The results show that the high drought tolerance and recovery after rehydration are the reasons for the normal growth of I. difengpi in karst mountain areas.

Drought-Stress-Induced Changes in Chloroplast Gene Expression in Two Contrasting Strawberry Tree (Arbutus unedo L.) Genotypes

This study investigated the effect of drought stress on the expression of chloroplast genes in two different genotypes (A1 and A4) of strawberry tree plants with contrasting performances. Two-year-old plants were subjected to drought (20 days at 18% field capacity), and the photosynthetic activity, chlorophyll content, and expression levels of 16 chloroplast genes involved in photosynthesis and metabolism-related enzymes were analyzed. Genotype-specific responses were prominent, with A1 displaying wilting and leaf curling, contrasting with the mild symptoms observed in A4. Quantification of damage using the net CO2 assimilation rates and chlorophyll content unveiled a significant reduction in A1, while A4 maintained stability. Gene expression analysis revealed substantial downregulation of A1 (15 out of 16 genes) and upregulation of A4 (14 out of 16 genes). Notably, psbC was downregulated in A1, while it was prominently upregulated in A4. Principal Component Analysis (PCA) highlighted genotype-specific clusters, emphasizing distinct responses under stress, whereas a correlation analysis elucidated intricate relationships between gene expression, net CO2 assimilation, and chlorophyll content. Particularly, a positive correlation with psaB, whereas a negative correlation with psbC was found in genotype A1. Regression analysis identified potential predictors for net CO2 assimilation, in particular psaB. These findings contribute valuable insights for future strategies targeting crop enhancement and stress resilience, highlighting the central role of chloroplasts in orchestrating plant responses to environmental stressors, and may contribute to the development of drought-tolerant plant varieties, which are essential for sustaining agriculture in regions affected by water scarcity.

Predicting transcriptional responses to heat and drought stress from genomic features using a machine learning approach in rice

Plants have evolved various mechanisms to adapt to adverse environmental stresses, such as the modulation of gene expression. Expression of stress-responsive genes is controlled by specific regulators, including transcription factors (TFs), that bind to sequence-specific binding sites, representing key components of cis-regulatory elements and regulatory networks. Our understanding of the underlying regulatory code remains, however, incomplete. Recent studies have shown that, by training machine learning (ML) algorithms on genomic sequence features, it is possible to predict which genes will transcriptionally respond to a specific stress. By identifying the most important features for gene expression prediction, these trained ML models allow, in theory, to further elucidate the regulatory code underlying the transcriptional response to abiotic stress. Here, we trained random forest ML models to predict gene expression in rice (Oryza sativa) in response to heat or drought stress. Apart from thoroughly assessing model performance and robustness across various input training data, the importance of promoter and gene body sequence features to train ML models was evaluated. The use of enriched promoter oligomers, complementing known TF binding sites, allowed us to gain novel insights in DNA motifs contributing to the stress regulatory code. By comparing genomic feature importance scores for drought and heat stress over time, general and stress-specific genomic features contributing to the performance of the learned models and their temporal variation were identified. This study provides a solid foundation to build and interpret ML models accurately predicting transcriptional responses and enables novel insights in biological sequence features that are important for abiotic stress responses.

"Millet Models" for harnessing nuclear factor-Y transcription factors to engineer stress tolerance in plants: current knowledge and emerging paradigms

MAIN CONCLUSION

The main purpose of this review is to shed light on the role of millet models in imparting climate resilience and nutritional security and to give a concrete perspective on how NF-Y transcription factors can be harnessed for making cereals more stress tolerant. Agriculture faces significant challenges from climate change, bargaining, population, elevated food prices, and compromises with nutritional value. These factors have globally compelled scientists, breeders, and nutritionists to think of some options that can combat the food security crisis and malnutrition. To address these challenges, mainstreaming the climate-resilient and nutritionally unparalleled alternative crops like millet is a key strategy. The C4 photosynthetic pathway and adaptation to low-input marginal agricultural systems make millets a powerhouse of important gene and transcription factor families imparting tolerance to various kinds of biotic and abiotic stresses. Among these, the nuclear factor-Y (NF-Y) is one of the prominent transcription factor families that regulate diverse genes imparting stress tolerance. The primary purpose of this article is to shed light on the role of millet models in imparting climate resilience and nutritional security and to give a concrete perspective on how NF-Y transcription factors can be harnessed for making cereals more stress tolerant. Future cropping systems could be more resilient to climate change and nutritional quality if these practices were implemented.

Overexpression of NtGCN2 improves drought tolerance in tobacco by regulating proline accumulation, ROS scavenging ability, and stomatal closure

Drought stress is a severe threat to plants. Genes that respond to drought stress are essential for plant growth and development. General control nonderepressible 2 (GCN2) encodes a protein kinase that responds to various biotic and abiotic stresses. However, the mechanism of GCN2 in plant drought tolerance remains unclear. In the present study, the promoters of NtGCN2 from Nicotiana tabacum K326, which contained a drought-responsive Cis-acting element MYB that can be activated by drought stress, were cloned. Furthermore, the drought tolerance function of NtGCN2 was investigated using NtGCN2-overexpressed transgenic tobacco plants. NtGCN2-overexpressed transgenic plants were more tolerant to drought stress than wild-type (WT) plants. The transgenic tobacco plants exhibited higher proline and abscisic acid (ABA) contents, antioxidant enzyme activities, leaf relative water content, and expression levels of genes encoding key antioxidant enzymes and proline synthase, but lower levels of malondialdehyde and reactive oxygen species, and reduced stomatal apertures, stomatal densities, and stomatal opening rates compared to WT plants under drought stress. These results indicated that overexpression of NtGCN2 conferred drought tolerance in transgenic tobacco plants. RNA-seq analysis showed that overexpression of NtGCN2 responded to drought stress by regulating the expression of genes related to proline synthesis and catabolism, abscisic acid synthesis and catabolism, antioxidant enzymes, and ion channels in guard cells. These results showed that NtGCN2 might regulate drought tolerance by regulating proline accumulation, reactive oxygen species (ROS) scavenging, and stomatal closure in tobacco and may have the potential for application in the genetic modification of crop drought tolerance.