Biofuel Potential of Plants Transformed Genetically with NAC Family Genes

WRKY Transcription Factors Modulate the Flavonoid Pathway of Rhododendron chrysanthum Pall. Under UV-B Stress

The depletion of the ozone layer has resulted in elevated ultraviolet-B (UV-B) radiation levels, posing a significant risk to terrestrial plant growth. Rhododendron chrysanthum Pall. (R. chrysanthum), adapted to high-altitude and high-irradiation environments, has developed unique adaptive mechanisms. This study exposed R. chrysanthum to UV-B radiation for two days, with an 8 h daily treatment, utilizing metabolomic and transcriptomic analyses to explore the role of WRKY transcription factors in the plant's UV-B stress response and their regulation of flavonoid synthesis. UV-B stress resulted in a significant decrease in rETR and Ik and a significant increase in 1-qP. These chlorophyll fluorescence parameters indicate that UV-B stress impaired photosynthesis in R. chrysanthum. Faced with the detrimental impact of UV-B radiation, R. chrysanthum is capable of mitigating its effects by modulating its flavonoid biosynthetic pathways to adapt positively to the stress. This study revealed changes in the expression of 113 flavonoid-related metabolites and 42 associated genes, with WRKY transcription factors showing significant correlation with these alterations. WRKY transcription factors can influence the expression of key enzyme genes in the flavonoid metabolic pathway, thereby affecting metabolite production. A theoretical reference for investigating plant stress physiology is provided in this work, which also offers insights into the stress responses of alpine plants under adverse conditions.

DET1 modulates ATAF1-repressed thermosensory elongation through ubiquitination in Arabidopsis

KEY MESSAGE

The Arabidopsis transcription factor ATAF1 negatively regulates thermomorphogenesis by inhibiting the expression of key genes involved in thermoresponsive elongation. DET1-mediated ubiquitination promotes ATAF1 degradation. In response to warmer, non-stressful average temperatures, plants have evolved an adaptive morphologic response called thermomorphogenesis to increase their fitness. This adaptive morphologic development is regulated by transcription factors (TFs) that control the expression of heat-induced genes that gate thermoresponsive growth. No apical meristem (NAM), Arabidopsis thaliana-activating factor 1/2 (ATAF1/2), and cup-shaped cotyledon 2 (CUC2) (collectively known as NAC) TFs regulate morphogenesis and respond to temperature stress, but whether they regulate thermomorphogenesis remains largely unknown. Here, we identified ATAF1 as a negative regulator of thermomorphogenesis and revealed that the E3-ligase component de-etiolated 1 (DET1) mediated ATAF1 ubiquitination and degradation. Our results revealed that ATAF1 negatively regulates warm temperature-induced hypocotyl elongation and inhibits the expression of thermoresponsive genes. Moreover, ATAF1 directly targeted and repressed the expression of YUCCA 8 (YUC8) and phytochrome interacting factor 4 (PIF4), two key regulators involved in elongation. At the post-translational level, elevated ambient temperatures negatively modulated the stability of ATAF1 by inducing the DET1-mediated ubiquitination pathway. Our results demonstrated the presence of a DET1-ATAF1-PIF4/YUC8 control module for thermomorphogenesis in plants, which may increase fitness by fine-tuning thermoresponsive gene expression under warm temperatures.

ScRNA-seq reveals dark- and light-induced differentially expressed gene atlases of seedling leaves in Arachis hypogaea L

Although the regulatory mechanisms of dark and light-induced plant morphogenesis have been broadly investigated, the biological process in peanuts has not been systematically explored on single-cell resolution. Herein, 10 cell clusters were characterized using scRNA-seq-identified marker genes, based on 13 409 and 11 296 single cells from 1-week-old peanut seedling leaves grown under dark and light conditions. 6104 genes and 50 transcription factors (TFs) displayed significant expression patterns in distinct cell clusters, which provided gene resources for profiling dark/light-induced candidate genes. Further pseudo-time trajectory and cell cycle evidence supported that dark repressed the cell division and perturbed normal cell cycle, especially the PORA abundances correlated with 11 TFs highly enriched in mesophyll to restrict the chlorophyllide synthesis. Additionally, light repressed the epidermis cell developmental trajectory extending by inhibiting the growth hormone pathway, and 21 TFs probably contributed to the different genes transcriptional dynamic. Eventually, peanut AHL17 was identified from the profile of differentially expressed TFs, which encoded protein located in the nucleus promoted leaf epidermal cell enlargement when ectopically overexpressed in Arabidopsis through the regulatory phytohormone pathway. Overall, our study presents the different gene atlases in peanut etiolated and green seedlings, providing novel biological insights to elucidate light-induced leaf cell development at the single-cell level.

Phenotypic and transcriptomic shifts in roots and leaves of rice under the joint stress from microplastic and arsenic

Co-contamination of soil from microplastics (MP) and arsenic (As) is becoming more prevalent, posing a severe threat to agricultural productivity. However, how this joint pollution affects crop growth needs to be better understood. To assess this, we investigated the transcriptomic and phenotypic patterns of rice (Oryza sativa) to MP, As, and their mixtures. The results revealed that, compared to As, MP had much less impact on rice growth, while the MP-As mixture decreased rice's aboveground biomass and altered As's biodistribution in rice tissues. Transcriptome further corroborated this pattern: 13 (294), 4195 (1842), and 3112 (2063) genes differentially regulated in response to MP, As, and their mixtures were observed in root (leaf) tissues, respectively. The joint application of MP and As produced a synergistic effect on crucial metabolic processes, such as carbohydrate, carboxylic acid, oxoacid, organic acid, amino acid, and tetrapyrrole metabolism. Moreover, we found that the joint stress reprogrammed the expression of hub genes encoding photosynthetic enzymes, protein kinases, and transcription factors, which likely reflect a transcript-driven tradeoff strategy between rice growth and defense. Together, these results strongly indicate that MP aggravated the As-induced toxicity in rice plants, which may impact the crop's acclimation to other abiotic field environments.

Cis-Regulation by NACs: A Promising Frontier in Wheat Crop Improvement

Crop traits are controlled by multiple genes; however, the complex spatio-temporal transcriptional behavior of genes cannot be fully understood without comprehending the role of transcription factors (TFs) and the underlying mechanisms of the binding interactions of their cis-regulatory elements. NAC belongs to one of the largest families of plant-specific TFs and has been associated with the regulation of many traits. This review provides insight into the cis-regulation of genes by wheat NACs (TaNACs) for the improvement in yield-related traits, including phytohormonal homeostasis, leaf senescence, seed traits improvement, root modulation, and biotic and abiotic stresses in wheat and other cereals. We also discussed the current potential, knowledge gaps, and prospects of TaNACs.

Transcriptome profiling reveals key genes in regulation of the tepal trichome development in Lilium pumilum D.C

A number of potential genes and pathways involved in tepal trichome development were identified in a natural lily mutant by transcriptome analysis and were confirmed with trichome and trichomeless species. Trichome is a specialized structure found on the surface of the plant with an important function in survival against abiotic and biotic stress. It is also an important economic trait in crop breeding. Extensive research has investigated the foliar trichome in model plants (Arabidopsis and tomato). However, the developmental mechanism of tepal trichome remains elusive. Lilium pumilum is an edible ornamental bulb and a good breeding parent possessing cold and salt-alkali resistance. Here, we found a natural mutant of Lilium pumilum grown on a highland whose tepals are covered by trichomes. Our data indicate that trichomes of the mutant are multicellular and branchless. Notably, stomata are also developed on the tepal of the mutant as well, suggesting there may be a correlation between trichome and stomata regulation. Furthermore, we isolated 27 differentially expressed genes (DEGs) by comparing the transcriptome profiling between the natural mutant and the wild type. These 27 genes belong to 4 groups: epidermal cell cycle and division, trichome morphogenesis, stress response, and transcription factors. Quantitative real-time PCR in Lilium pumilum (natural mutant and the wild type) and other lily species (Lilium leichtlinii var. maximowiczii/trichome; Lilium davidii var. willmottiae/, trichomeless) confirmed the validation of RNA-seq data and identified several trichome-related genes.

The biotechnological importance of the plant-specific NAC transcription factor family in crop improvement

Climate change, malnutrition, and food insecurity are the inevitable challenges being faced by the agriculture sector today. Plants are susceptible to extreme temperatures during the crucial phases of flowering and seed development, and elevated carbon levels also lead to yield losses. Productivity is also affected by floods and droughts. Therefore, increasing plant yield and stress tolerance are the priorities to be met through novel biotechnological interventions. The contributions of NAC genes towards enhancing plant survivability under stress is well known. Here we focus on the potential of NAC genes in the regulation of abiotic stress tolerance, secondary cell wall synthesis, lateral root development, yield potential, seed size and biomass, ROS signaling, leaf senescence, and programmed cell death. Once naturally tolerant candidate NAC genes have been identified, and the nature of their association with growth and fitness against multi-environmental stresses has been determined, they can be exploited for building inherent tolerance in future crops via transgenic technologies. An update on the latest developments is provided in this review, which summarizes the current understanding of the roles of NAC in the establishment of various stress-adaptive mechanisms in model and food crop plants.