Identification of the NAC Transcription Factors and Their Function in ABA and Salinity Response in Nelumbo nucifera

Genome-wide identification of NAC transcription factors in Acer paxii, and their expression dynamics during leaf aging

BACKGROUND

The NAC family (consisting of NAM, ATAF1/2, and CUC2) represents a crucial plant-specific transcription factor family, contributing significantly to various aspects of plant growth, development, and reactions to abiotic stresses. Yet, the underlying mechanism of NAC regulation in Acer paxii has not been discussed.

OBJECTIVES

Identification of NAC genes (ApNACs) in the genome of Acer paxii and exploring the regulatory network of NACs in mediating leaf senescence.

METHODS

A thorough genome-wide analysis of the NAC gene family in the Acer paxii genome was performed.

RESULTS

We identified 117 ApNACs from the Acer paxii genome database, which were irregularly distributed across 13 chromosomes. Phylogenetic analysis revealed that ApNAC genes were partitioned into 16 subgroups. There are four kinds of cis-regulatory elements in the promoter region of the ApNACs gene. We compared the expression levels of ApNAC genes at different times using transcriptome data and selected six ApNAC genes for qRT-PCR, which the results showed basic consistency with the transcriptome results. Six ApNACs and 187 TFs from different families were selected, and it was found that the TF families with the highest correlation were WRKY, MYB, bZIP, and ERF, and these TF families were reported to participate in the regulation function in senescence.

CONCLUSION

This study provides important data support for identifying the NAC gene family of Acer paxii and the regulatory function of the ApNAC genes on plant senescence, which will help to understand the NAC-mediated regulatory network in Acer paxii.

The transcription factor NnNAC100 positively regulates amylopectin biosynthesis by activating NnSBEII in the rhizome of Nelumbo nucifera Gaertn

KEY MESSAGE

NnNAC100-NnSBEII modules enhance starch content of the rhizome in Nelumbo nucifera Gaertn. Nelumbo nucifera Gaertn. is a popular aquatic vegetable and traditional Chinese medicine whose quality and taste are mainly determined by the starch. Although starch-related genes have been functionally characterized, the regulated mechanism of enzyme (SBE) remains unclear. In this study, we identified and functionally elucidated the functions of NnSBEII and NnNAC100 using transient overexpression of NnSBEII and NnNAC100 in rhizomes of lotus, and it significantly increased the amylopectin content and total starch content. Accordingly, functional complementation assay in defective Arabidopsis also showed that NnSBEII compensated for the low content of starch in the mutant sbe2.2. In addition, overexpression of NnSBEII and NnNAC100 significantly increased the content of starch in transgenic lines. Consistently, opposite results were observed under the background of repressed NnSBEII and NnNAC100 in rhizomes of lotus. Furthermore, yeast one-hybrid and dual-luciferase assays revealed that NnNAC100 could directly bind to the NnSBEII promoter and promote the expression of NnSBEII. Transient overexpression of NnNAC100 upregulated NnSBEII expression significantly, while the expression level of AtSBE2.2 in transgenic Arabidopsis overexpressing NnNAC100 was higher than that of WT, which indicated that NnNAC100 promoted the synthesis of amylopectin by enhancing the expression of NnSBEII. In addition, we found that NnSBEII could form a complex protein by interacting with soluble starch synthase (NnSS2) to increase the activity of the SBEII enzyme. These results reveal a novel mechanism that the NnNAC100-NnSBEII-NnSBEII/NnSS2 module regulates amylopectin biosynthesis and these will provide insights into the broader implications of the regulation mechanism of starch biosynthesis.

Genome-Wide Identification and Expression Analysis of NAC Gene Family Members in Seashore Paspalum Under Salt Stress

The NAC gene family plays a crucial role in plant growth, development, and responses to biotic and abiotic stresses. Paspalum Vaginatum, a warm-season turfgrass with exceptional salt tolerance, can be irrigated with seawater. However, the NAC gene family in seashore paspalum remains poorly understood. In this study, genome-wide screening and identification were conducted based on the NAC (NAM) domain hidden Markov model in seashore paspalum, resulting in the identification of 168 PvNAC genes. A phylogenetic tree was constructed, and the genes were classified into 18 groups according to their topological structure. The physicochemical properties of the PvNAC gene family proteins, their conserved motifs and structural domains, cis-acting elements, intraspecific collinearity analysis, GO annotation analysis, and protein-protein interaction networks were analyzed. The results indicated that the majority of PvNAC proteins are hydrophilic and predominantly localized in the nucleus. The promoter regions of PvNACs are primarily enriched with light-responsive elements, ABRE motifs, MYB motifs, and others. Intraspecific collinearity analysis suggests that PvNACs may have experienced a large-scale gene duplication event. GO annotation indicated that PvNAC genes were essential for transcriptional regulation, organ development, and responses to environmental stimuli. Furthermore, the protein interaction network predicted that PvNAC73 interacts with proteins such as BZIP8 and DREB2A to form a major regulatory hub. The transcriptomic analysis investigates the expression patterns of NAC genes in both leaves and roots under varying durations of salt stress. The expression levels of 8 PvNACs in roots and leaves under salt stress were examined and increased to varying degrees under salt stress. The qRT-PCR results demonstrated that the expression levels of the selected genes were consistent with the FPKM value trends observed in the RNA-seq data. This study established a theoretical basis for understanding the molecular functions and regulatory mechanisms of the NAC gene family in seashore paspalum under salt stress.

Elucidation of PGPR-responsive OsNAM2 regulates salt tolerance in Arabidopsis by AFP2 and SUS protein interaction

This study investigates the molecular mechanisms underlying salt stress responses in plants, focusing on the regulatory roles of OsNAM2, a gene influenced by the plant growth-promoting rhizobacterium Bacillus amyloliquefaciens (SN13). The study examines how SN13-modulated OsNAM2 enhances salt tolerance in Arabidopsis through physiological, biochemical, and molecular analyses. Overexpression of OsNAM2, especially with SN13 inoculation, improves germination, seedling growth, root length, and biomass under high NaCl concentrations compared to wild-type plants, indicating a synergistic effect. OsNAM2 overexpression enhances relative water content, reduces electrolyte leakage and malondialdehyde accumulation, and increases proline content, suggesting better membrane integrity and stress endurance. Furthermore, SN13 and OsNAM2 overexpression modulates essential metabolic genes involved in glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle, facilitating metabolic adjustments crucial for salt stress adaptation. The interaction of OsNAM2 with SUS, facilitated by SN13, suggests enhanced sucrose metabolism efficiency, providing substrates for protective responses. Additionally, OsNAM2 plays a regulatory role in the ABA signaling pathway through significant protein-protein interactions like with AFP2. This study highlights the intricate interplay between SN13-responsive OsNAM2 and key signaling pathways, suggesting strategies for enhancing crop salt tolerance through targeted genetic and microbial interventions.

Transporters and phytohormones analysis reveals differential regulation of ryegrass (Lolium perenne L.) in response to cadmium and arsenic stresses

Cadmium (Cd) and arsenic (As) are two highly toxic heavy metals and metalloids that coexist in many situations posing severe threats to plants. Our investigation was conducted to explore the different regulatory mechanisms of ryegrass (Lolium perenne L.) responding to individual and combined Cd and As stresses in hydroponics. Results showed that the ryegrass well-growth phenotype was not affected by Cd stress of 10 mg·L-1. However, As of 10 mg·L-1 caused rapid water loss, proline surge, and chlorosis in shoots, suggesting that ryegrass was highly sensitive to As. Transcriptomic analysis revealed that the transcription factor LpIRO2 mediated the upregulation of ZIP1 and YSL6 that played an important role in Cd tolerance. We found that the presence of As caused the overexpression of LpSWT12, a process potentially regulated by bHLH14, to mitigate hyperosmolarity. Indoleacetic acid (IAA) and abscisic acid (ABA) contents and expression of their signaling-related genes were significantly affected by As stress rather than Cd. We predict a regulatory network to illustrate the interaction between transporters, transcription factors, and signaling transduction, and explain the antagonism of Cd and As toxicity. This present work provides a research basis for plant protection from Cd and As pollution.

Transcriptional Control of Seed Life: New Insights into the Role of the NAC Family

Transcription factors (TFs) regulate gene expression by binding to specific sequences on DNA through their DNA-binding domain (DBD), a universal process. This update conveys information about the diverse roles of TFs, focusing on the NACs (NAM-ATAF-CUC), in regulating target-gene expression and influencing various aspects of plant biology. NAC TFs appeared before the emergence of land plants. The NAC family constitutes a diverse group of plant-specific TFs found in mosses, conifers, monocots, and eudicots. This update discusses the evolutionary origins of plant NAC genes/proteins from green algae to their crucial roles in plant development and stress response across various plant species. From mosses and lycophytes to various angiosperms, the number of NAC proteins increases significantly, suggesting a gradual evolution from basal streptophytic green algae. NAC TFs play a critical role in enhancing abiotic stress tolerance, with their function conserved in angiosperms. Furthermore, the modular organization of NACs, their dimeric function, and their localization within cellular compartments contribute to their functional versatility and complexity. While most NAC TFs are nuclear-localized and active, a subset is found in other cellular compartments, indicating inactive forms until specific cues trigger their translocation to the nucleus. Additionally, it highlights their involvement in endoplasmic reticulum (ER) stress-induced programmed cell death (PCD) by activating the vacuolar processing enzyme (VPE) gene. Moreover, this update provides a comprehensive overview of the diverse roles of NAC TFs in plants, including their participation in ER stress responses, leaf senescence (LS), and growth and development. Notably, NACs exhibit correlations with various phytohormones (i.e., ABA, GAs, CK, IAA, JA, and SA), and several NAC genes are inducible by them, influencing a broad spectrum of biological processes. The study of the spatiotemporal expression patterns provides insights into when and where specific NAC genes are active, shedding light on their metabolic contributions. Likewise, this review emphasizes the significance of NAC TFs in transcriptional modules, seed reserve accumulation, and regulation of seed dormancy and germination. Overall, it effectively communicates the intricate and essential functions of NAC TFs in plant biology. Finally, from an evolutionary standpoint, a phylogenetic analysis suggests that it is highly probable that the WRKY family is evolutionarily older than the NAC family.

Overexpression of a Fragaria vesca NAM, ATAF, and CUC (NAC) Transcription Factor Gene (FvNAC29) Increases Salt and Cold Tolerance in Arabidopsis thaliana

The NAC (NAM, ATAF1/2, CUC2) family of transcription factors (TFs) is a vital transcription factor family of plants. It controls multiple parts of plant development, tissue formation, and abiotic stress response. We cloned the FvNAC29 gene from Fragaria vesca (a diploid strawberry) for this research. There is a conserved NAM structural domain in the FvNAC29 protein. The highest homology between FvNAC29 and PaNAC1 was found by phylogenetic tree analysis. Subcellular localization revealed that FvNAC29 is localized onto the nucleus. Compared to other tissues, the expression level of FvNAC29 was higher in young leaves and roots. In addition, Arabidopsis plants overexpressing FvNAC29 had higher cold and high-salinity tolerance than the wild type (WT) and unloaded line with empty vector (UL). The proline and chlorophyll contents of transgenic Arabidopsis plants, along with the activities of the antioxidant enzymes like catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) under 200 mM NaCl treatment or -8 °C treatment, were higher than those activities of the control. Meanwhile, malondialdehyde (MDA) and the reactive oxygen species (ROS) content were higher in the WT and UL lines. FvNAC29 improves transgenic plant resistance to cold and salt stress by regulating the expression levels of AtRD29a, AtCCA1, AtP5CS1, and AtSnRK2.4. It also improves the potential to tolerate cold stress by positively regulating the expression levels of AtCBF1, AtCBF4, AtCOR15a, and AtCOR47. These findings suggest that FvNAC29 may be related to the processes and the molecular mechanisms of F. vesca response to high-salinity stress and LT stress, providing a comprehensive understanding of the NAC TFs.

Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Gene Family in Litchi chinensis

NAC proteins play an essential role in the growth and development of litchi, especially during reproductive development. However, a comprehensive analysis of the litchi NAC gene family is currently absent. Based on information from the litchi genome, we found that the 112 NAC genes of litchi show an uneven distribution on the chromosomes. Phylogenetic and conserved structural domain analyses indicated that different types of variability were exhibited in the family of litchi NACs (LcNACs). Gene covariance analysis showed that the LcNACs showed better similarity in the same genus than with Arabidopsis. We further investigated the differential expression patterns of LcNACs in buds and rudimentary leaves of litchi. qRT-PCR results implied that they were involved in the process. Profiling of LcNAC promoter elements in litchi showed that they were extensively involved in light response, phytohormone regulation, abiotic stress response, and plant growth and development processes. This study provides new insights into the identification, structural characterization, tissue-specific expression analysis, and promoter response elements of LcNACs. It reveals the characteristics of the LcNACs and lays the foundation for the subsequent understanding of its biological functions and molecular regulatory mechanisms.

Exploration of the Regulatory Pathways and Key Genes Involved in the Response to Saline-Alkali Stress in Betula platyphylla via RNA-Seq Analysis

The pH of saline-alkali soil is high because of carbonate salts, and the deleterious effects of saline-alkali soil on the growth of plants are greater than those of saline soil. Few studies have examined the saline-alkali tolerance of Betula platyphylla at the molecular level. To clarify the regulatory mechanism underlying saline-alkali tolerance in B. platyphylla, RNA sequencing analysis of B. platyphylla seedlings treated with NaHCO₃ was conducted. Differences in gene expression in the roots of B. platyphylla seedlings under saline-alkali stress (induced via NaHCO₃) for 3 h and 6 h were characterized, and a total of 595 and 607 alkali stress-responsive genes were identified, respectively. Most differentially expressed genes were involved in stress, signal transduction, secondary metabolic process, regulation of jasmonic acid, and the abiotic stimulus signaling pathway. The single nucleotide polymorphism loci in the differentially expressed genes were associated with the alkaline-salt tolerance in birch germplasm. In addition, birch plants overexpressing WRKY70 and NAC9 were obtained using the A. tumefaciens-mediated transient transformation method, and these two genes were found to play key roles in saline-alkali tolerance. Additional study revealed that WRKY70 and NAC9 can increase resistance to saline-alkali stress by enhancing reactive oxygen species scavenging and inhibiting cell death in birch plants. The results of this study enhance our understanding of the saline-alkali stress tolerance of B. platyphylla at the molecular level, and provide several key genes that could be used in the breeding of birch plants in the future.