NACs, generalist in plant life

VvNAC33 functions as a key regulator of drought tolerance in grapevine by modulating reactive oxygen species production

Grapevine (Vitis vinifera L. and other Vitis spp.) is an important economic crop, but its yield and quality are severely affected by drought stress. NAC transcription factors, which play key roles in plant stress responses, have remained largely unexplored in grapevine drought tolerance. This study identified VvNAC33 as a drought-responsive candidate gene through transcriptomic analysis and demonstrated its role as a positive regulator of drought tolerance. VvNAC33 expression was significantly upregulated under drought stress. Subcellular localization and transcriptional activity analyses confirmed its nuclear localization and transcriptional activation potential. Overexpression of VvNAC33 in Arabidopsis thaliana and transient overexpression in grapevine enhanced drought tolerance, whereas virus-induced gene silencing increased drought sensitivity. This enhanced tolerance was associated with the activation of the antioxidant defense system, including superoxide dismutase, peroxidase, and catalase, which promoted reactive oxygen species scavenging and alleviated oxidative damage. The enhanced expression of VvCAT1, VvCu/ZnSOD, and VvPOD4 by VvNAC33 highlights its crucial role in regulating antioxidant gene expression under drought stress. These findings strongly support the role of VvNAC33 in drought tolerance and identify it as a potential molecular target for enhancing drought resistance in grapevine.

Strategies to develop climate-resilient chili peppers: transcription factor optimization through genome editing

Chili peppers (Capsicum spp.), a globally significant crop revered for their nutritional, economic, and cultural importance, are increasingly imperiled by the converging burdens of climate-induced abiotic stresses, including drought, heat, and salinity, and relentless biotic assaults from pathogens and insect herbivores. These overlapping stressors not only destabilize yield but also compromise the metabolic intricacy responsible for the accumulation of health-promoting secondary metabolites. Although Capsicum exhibits remarkable genetic and phytochemical diversity, the integrated transcriptional, metabolic, and epigenetic frameworks that underpin its stress resilience remain poorly delineated. This review synthesizes recent advances in decoding core transcription factor families, such as CaNAC, CaWRKY, and CaMYB, that serve as pivotal regulators of osmotic adjustment, reactive oxygen species detoxification, hormonal crosstalk, and secondary metabolite biosynthesis under stress conditions. We further highlight how multi-omics-guided gene discovery, when paired with CRISPR/Cas-mediated genome editing, enables precise reprogramming of key regulatory loci to enhance adaptive responses. Emerging innovations, including base editing, prime editing, and novel nucleases like Cas12a and Cas13d, are expanding the functional genome-editing landscape, while the integration of morphogenic regulators and genotype-independent transformation platforms is beginning to circumvent long-standing obstacles in Capsicum genetic engineering. Lastly, we propose a transformative framework that converges transcription factor modulation, multi-omics strategies, precision phenotyping, and next-generation genome editing to accelerate the development of climate-resilient Capsicum cultivars with optimized metabolic traits. This strategic convergence of molecular insight and biotechnological innovation offers a robust foundation for building next-generation chili pepper varieties capable of withstanding intensifying environmental and pathogenic pressures, ultimately safeguarding yield, nutritional quality, and agricultural sustainability in the face of global climate change.

MdNAC2 enhances K+ deficiency stress tolerance by maintaining K+ homeostasis in apple

Potassium (K) is an essential nutrient for apple production, with its deficiency severely compromising yield and fruit quality. The development of K deficiency-resistant rootstocks represents an effective and promising approach to alleviating the adverse effects of K deficiency stress. However, the molecular mechanisms underlying apple resistance to K deficiency remain poorly understood. Here, we identified the transcription factor MdNAC2 as a critical regulator of apple tolerance to K deficiency through RNA-seq using Malus hupehensis as material. MdNAC2 enhanced apple tolerance to K deficiency by maintaining K+ homeostasis, primarily through directly suppressing the expression of the K+ efflux transporter MdGORK1. This regulatory mechanism reduces K+ efflux and stabilizes intracellular K+ levels under K deficiency stress. Collectively, our findings highlight the pivotal role of the MdNAC2-MdGORK1-K+ regulatory module in maintaining K+ and conferring apple resistance to K deficiency. This study provides new insights into the molecular mechanisms of K deficiency tolerance and establishes a theoretical foundation for breeding K deficiency-resistant apple rootstocks and cultivars.

Genome-wide identification and expression profiles of NAC transcription factors in Poncirus trifoliata reveal their potential roles in cold tolerance

BACKGROUND

Citrus, a globally vital economic crop, faces severe challenges due to extreme climatic conditions and diseases/pests attack. Poncirus trifoliata is closely related to citrus and shows unique cold tolerance, making it a crucial material for unraveling genes involved in cold tolerance. NAC (NAM, ATAF1/2, CUC2) transcription factors play important roles in plant growth, development, and stress responses. However, their evolution patterns and gene functions in citrus remain poorly studied. This study aims to elucidate the genomic characteristics and evolution of the NAC genes in P. trifoliata, and to analyze their expression patterns and conduct functional validation under cold stress.

RESULTS

Genome-wide analysis identified 135 PtrNAC genes in P. trifoliata with non-random chromosomal distribution, including 20 gene clusters. 57.78% of the NAC genes are located in the chromosomes 3, 4 and 5. Gene duplication analysis revealed that proximal and tandem duplications as primary expansion mechanisms, with tandem repeats specifically driving gene expansion in citrus lineages (subfamilies IV, V, and VII). Collinearity analysis showed that 24.44% of the PtrNAC genes were retained in homologous regions, and Ka/Ks ratio analysis further confirmed that purifying selection dominated their evolutionary process. Transcriptome landscapes revealed that Pt5g024390 (PtrNAC2) was induced to the greatest degree under the cold stress. Meanwhile, expression level of PtrNAC2 in tetraploid was more than two folds higher compared to diploid counterpart in the presence of cold stress. Virus-induced gene silencing of PtrNAC2 led to significantly enhanced cold tolerance, implying that it plays a negative role in regulation of cold tolerance.

CONCLUSION

This study systematically elucidated the global distribution and evolutionary patterns of NAC genes in P. trifoliata. In addition, the NAC gene exhibit adaptive expansion driven by tandem duplications. The identification of PtrNAC2, a negative regulator of cold tolerance in P. trifoliata, provides valuable insights into unravelling potential candidates for engineering cold tolerance in citrus.

Genome-Wide Identification of 109 NAC Genes and Dynamic Expression Profiles Under Cold Stress in Madhuca longifolia

Madhuca longifolia (M. longifolia), a tropical tree valued for its medicinal, nutritional, and industrial applications, exhibits severe sensitivity to low-temperature stress in subtropical regions, particularly during seedling establishment. To address this challenge, this study systematically identified 109 NAC genes in M. longifolia and characterized their functional roles in cold adaptation via multi-omics analyses. All NAC proteins were hydrophilic. Key members (e.g., MlNAC026, MlNAC077, MlNAC076) were localized in the nucleus. Phylogenetic analysis grouped them with ANAC072 (RD26), a homolog involved in leaf senescence and ABA-regulated cold stress responses. The NAC family expanded primarily through segmental duplication. And low Ka/Ks ratios (<1) indicated purifying selection. Promoter analysis highlighted the prevalence of dehydration-responsive DRE and LTR cis-acting elements. Transcriptomic profiling under cold stress identified five continuous differentially expressed genes (MlNAC026, MlNAC040, MlNAC059, MlNAC077, and MlNAC078) linked to regulatory functions. Homology modeling predicted 3D structures of cold-responsive NAC proteins, and STRING network analysis indicated independent regulatory mechanisms due to the absence of prominent interaction nodes. These findings advance our understanding of NAC-mediated cold tolerance and offer genetic targets to enhance M. longifolia resilience in subtropical climates.

JUNGBRUNNEN1, a Central Regulator of Plant Growth and Stress Response

Plants are under constant pressure to cope with ever-changing environmental conditions, requiring them to regulate their growth and stress response precisely. Transcription factors are key players in integrating stress-derived signals into developmental programs. One such transcription factor, JUNGBRUNNEN1 (JUB1), a member of the NAC family, has been identified as a central regulator of plant growth and stress responses. In this review, we discuss the structure of JUB1 and its recently identified alternatively spliced form and explore their potential modes of operation. We examine (i) how developmental and environmental cues regulate the expression of JUB1, (ii) its role as a negative regulator of leaf senescence while modulating tolerance to multiple abiotic and biotic stresses, and (iii) its function in regulating the trade-off between plant growth and defense. Furthermore, we provide insights into the regulation of JUB1, its interacting partners, and the potential conservation of its regulatory role across land plants. Given the climate crisis, we highlight the importance of identifying multitudinous stress response regulators such as JUB1 and emphasize the potential of its homologues in several important crop plants. Optimizing its application could make it an invaluable resource for improving crop resilience under changing climatic conditions.

Two Master Transcription Factors for Fruit Ripening, NOR and Its Homologue NOR-like1: Multiple Roles in tomato

Non-ripening (NOR) and NOR-like1, two members of the tomato NAC transcription factor (TF) family, exhibit a high degree of homology and are well-recognized for their robust control of fruit ripening. The discovery of NOR and NOR-like1 has greatly advanced our understanding of the regulation of tomato fruit ripening and their function studies beyond fruit ripening. This review systematically summarizes the current perception of nor natural mutant (nor mutant), as well as the roles of NOR and NOR-like1 in tomato fruit ripening and beyond. Additionally, this review highlights the functional similarity and divergence of NOR and NOR-like1. In summary, we discuss the functional diversity and underlying mechanisms of NOR and NOR-like1 in tomato and propose a molecular regulatory network dominated by NOR and NOR-like1.

NAC Transcription Factor GmNAC035 Exerts a Positive Regulatory Role in Enhancing Salt Stress Tolerance in Plants

Soybean, a globally significant and versatile crop, serves as a vital source of both oil and protein. However, environmental factors such as soil salinization pose substantial challenges to its cultivation, adversely affecting both yield and quality. Enhancing the salt tolerance of soybeans can mitigate yield losses and promote the development of the soybean industry. Members of the plant-specific transcription factor family NAC play crucial roles in plant adaptation to abiotic stress conditions. In this study, we screened the soybean GmNAC family genes potentially involved in the salt stress response and identified 18 GmNAC genes that may function during the early stages of salt stress. Among these, the GmNAC035 gene exhibited a rapid increase in expression within one hour of salt treatment, with its expression being induced by abscisic acid (ABA) and methyl jasmonate (MeJA), suggesting its significant role in the soybean salt stress response. We further elucidated the role of GmNAC035 in soybean salt tolerance. GmNAC035, a nuclear-localized transcriptional activator, enhances salt tolerance when overexpressed in Arabidopsis, reducing oxidative damage and boosting the expression of stress-responsive genes. It achieves this by regulating key stress response pathways, including the SOS pathway, calcium signaling, and ABA signaling. These findings highlight the potential of GmNAC035 as a genetic engineering target to improve crop salt tolerance.

IDD10-NAC079 transcription factor complex regulates sheath blight resistance by inhibiting ethylene signaling in rice

INTRODUCTION

Rhizoctonia solani Kühn is a pathogen causing rice sheath blight (ShB). Ammonium transporter 1 (AMT1) promotes resistance of rice to ShB by activating ethylene signaling. However, how AMT1 activates ethylene signaling remains unclear.

OBJECTIVE

In this study, the indeterminate domain 10 (IDD10)-NAC079 interaction model was used to investigate whether ethylene signaling is modulated downstream of ammonium signaling and modulates ammonium-mediated ShB resistance.

METHODS

RT-qPCR assay was used to identify the relative expression levels of nitrogen and ethylene related genes. Yeast two-hybrid assays, Bimolecular fluorescence complementation (BiFC) and Co-immunoprecipitation (Co-IP) assay were conducted to verify the IDD10-NAC079-calcineurin B-like interacting protein kinase 31 (CIPK31) transcriptional complex. Yeast one-hybrid assay, Chromatin immunoprecipitation (ChIP) assay, and Electrophoretic mobility shift assay (EMSA) were used to verify whether ETR2 was activated by IDD10 and NAC079. Ethylene quantification assay was used to verify ethylene content in IDD10 transgenic plants. Genetic analysis is used to detect the response of IDD10, NAC079 and CIPK31 to ShB infestation.

RESULTS

IDD10-NAC079 forms a transcription complex that activates ETR2 to inhibit the ethylene signaling pathway to negatively regulating ShB resistance. CIPK31 interacts and phosphorylates NAC079 to enhance its transcriptional activation activity. In addition, AMT1-mediated ammonium absorption and subsequent N assimilation inhibit the expression of IDD10 and CIPK31 to activate the ethylene signaling pathway, which positively regulates ShB resistance.

CONCLUSION

The study identified the link between ammonium and ethylene signaling and improved the understanding of the rice resistance mechanism.

Genome wide identification of LcC2DPs gene family in Lotus corniculatus provides insights into regulatory network in response to abiotic stresses

Low temperatures and drought reduce forage yield and quality, with protein kinases crucial for plant stress response. This study examines the LcC2DPs protein kinase family in Lotus corniculatus, identifying 90 members, with some tandemly distributed on chromosomes 2-6, and grouped into 5 subfamilies (I-V). 34 homologous gene pairs were found in Arabidopsis thaliana. LcC2DP genes promoters contain hormone and stress response elements. GO analysis highlights enrichment in hormone response and kinase activity. Transcriptomic analysis links 78 genes to environmental response and stress growth, with 10 validated by qRT-PCR after treatment with 100 μM ABA and IAA, 20% PEG6000, and 4 °C. Protein interaction analysis identifies 5 core proteins (LcC2DP5, 11, 15, 38, and 58) activated by drought and cold stress. Gene analysis revealed that only LcC2DP5 and LcC2DP15 share co-expression transcription factors, with bZIP, bHLH, WRKY, NAC, MYB-related, MYB, C3H, and C2H2 being prominent. These proteins are expressed under drought and cold conditions, highlighting LcC2DP5 and LcC2DP15 activity. NAC and C2H2 are vital for drought response, while bZIP and MYB-related are important for cold response. This suggests that various LcC2DPs in Lotus corniculatus respond to hormones and stress via a TF regulatory network.

Characterization of the NAC gene family in 'Fengdan' peony (Paeonia ostii) insights into the evolution and expression patterns under abiotic stresses and ABA treatment

Background

As one of the largest plant-specific transcription factor families, NAC proteins are crucial for plant growth and development processes and responses to various abiotic and biotic stresses. The published sequenced chromosome-level genome of 'Fengdan'peony provides a powerful tool for the analysis of the NAC gene family in this shrub.

Methods

The PoNAC gene family was identified and characterized using bioinformatic analysis, and RT-qPCR analysis was performed on some PoNACs from the ATAF and NAP subfamilies.

Results

In this study, a total of 82 NAC transcription factors (TFs) were identified in the 'Fengdan' peony genome, with the uneven anchorage of 78 PoNAC genes on 5 chromosomes, whereas only 4 PoNAC genes were found to be located on unanchored scaffolds. Through the phylogenetic analysis, 66 PoNAC genes were classified into 15 distinct subfamilies. The gene structure analysis revealed the variation in the number of exons from 0 to 14. Moreover, the motif analysis indicated that the identified PoNAC TFs possessed conserved NAC domains and motifs. The duplication events of PoNAC genes included whole-genome duplications (WGDs) or segmental duplications for 14 pairs, tandem duplications for 2 pairs, and proximal duplications for 3 pairs. GO analysis results suggested that the functions of PoNAC genes were mostly concentrated in the "biological process" GO category. Additionally, the analysis of the expression profiles of PoNAC genes in different plant organs revealed that only 45 genes were expressed in various tissues, some of them exhibited tissue-specific expression related to plant growth and development. RT-qPCR experiments demonstrated the responses of 8 genes from the ATAF and NAP subfamilies to ABA, heat and drought, suggesting that they may serve as important regulatory factor.

Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Transcription Factor Family in Sweet Cherry (Prunus avium L.)

The NAC (NAM, ATAF1/2, and CUC2) family is one of the largest plant-specific transcription factor families, playing a crucial role in adaptation to abiotic stresses. However, the NAC gene family in sweet cherry (Prunus avium L.) remains poorly understood. In this study, we identified 130 NAC genes (PaNAC) from the sweet cherry genome, which were unevenly distributed across eight chromosomes. Phylogenetic analysis classified the PaNACs into 21 distinct groups, including 2 sweet cherry-specific groups. Comparative analysis revealed significant variations in gene proportions, exon-intron structures, and motif compositions among different groups. Furthermore, cis-element analysis suggested the potential roles of PaNACs in regulating plant growth, development, hormone signaling, and stress responses. Transcriptomic data revealed tissue-specific expression patterns for several PaNAC genes. qRT-PCR further confirmed that eight selected PaNACs were responsive to various abiotic stresses in Gisela 6, a widely used hybrid rootstock in sweet cherry production that shares high sequence similarity in NAC genes with P. avium. These findings provide valuable insights for future research on the functional characteristics of the PaNAC genes in the growth, development, and responses to abiotic stress in sweet cherry.

AsNAC Genes: Response to High Mercury Concentrations in Allium sativum Seed Clove

Heavy metal contamination in soils is a growing concern due to anthropogenic activities, and Allium sativum (garlic) has shown tolerance to mercury pollution. We analyzed the physiological and molecular responses of garlic cloves exposed to HgCl2 at 0, 5000, 23,000, and 46,000 mg/kg for 2, 3, and 4 h. The germination percentage was lower than 46,000 mg/kg Hg for 4 h. We also analyzed the expression levels of NAC transcription factors and found that AsNAC11 had higher expression at 46,000 mg/kg at 2 h; AsNAC17 was underexpressed and the maximum was at 2 h at 23,000 mg/kg. AsNAC20 had the highest expression (30 times more than the control) at 3 and 4 h with 23,000 mg/Kg. AsNAC27 showed the highest expression at 3 h with 23,000 mg/kg. The tissues exhibited a maximum Hg bioconcentration factor of 0.037 at 23,000 mg/kg, indicating moderate mercury absorption. However, at a concentration of 46,000 mg/kg, the BCF decreased to 0.023. Our in-silico analysis revealed that the analyzed AsNACs are associated with various abiotic stress responses. This study provides valuable insights into genes that could be utilized for genetic improvement to enhance crop resistance to mercury soil contamination.

The NAC transcription factor PagNAC17 enhances salt tolerance in poplar by alleviating photosynthetic inhibition

The NAC transcription factor family is essential for plant growth, development, and stress responses. This study, based on RNA-Seq data from 84K poplar and weighted gene co-expression network analysis (WGCNA), identified PagNAC17 as a key factor in the salt stress response of poplar. A total of 202 PtrNAC TFs were identified and categorized into two major subfamilies, with their conserved motifs, gene structures, and cis-acting elements analyzed. Genes co-expressed with PagNAC17 are involved in energy metabolism, such as photosynthesis (e.g., light absorption and CO2 fixation), oxidative phosphorylation, signal transduction processes, and stress responses (e.g., the glutathione metabolism pathway), suggesting that PagNAC17 may regulate salt tolerance in poplar through these pathways. PagNAC17 is localized in the nucleus, primarily expressed in young leaves with the lowest expression in roots, and has transcriptional activation activity. The expression of PagNAC17 in yeast significantly enhances growth under salt conditions. Likewise, the overexpression of PagNAC17 in 84K poplar also significantly enhances salt tolerance, reducing yellowing, wilting, and oxidative damage. In summary, PagNAC17 is a key salt-tolerance regulator within the poplar NAC gene family. This study provides valuable insights for functional research on the NAC TFs family and offers a promising genetic resource for the salt-tolerance breeding of poplar.

Comparative transcriptomic and hormone analyses reveal the molecular mechanisms regulating almond flowering stages

Almond (Prunus dulcis) is cultivated worldwide and is valued for its flavourful seeds, which have significant economic value. In China, domestically cultivated almonds are primarily found in Shache County, Kashgar, Xinjiang. However, in this region, the flowering stages generally begin too early, such that almond blooms are vulnerable to low spring temperatures, which can damage or kill flower organs and severely affect fruit yield. To date, there have been no studies on the regulatory mechanisms involved in almond flowering. Therefore, we conducted transcriptomic and hormone analyses on six flower developmental stages in two almond cultivars-the primary Chinese cultivar Wanfeng and the primary American cultivar Nonpareil-to determine the molecular mechanisms regulating flowering. In Shache County, Wanfeng almond completed its entire flowering stage in just 16 days, whereas Nonpareil required 43 days. The results of the GO and KEGG enrichment analyses of the differentially expressed genes revealed that Nonpareil almond requires more photosynthesis and more nutrients to complete the flowering process. The photoperiod pathway and time-ordered gene coexpression network revealed that four flowering time genes, CDFs, GA2ox8, IAA7, and WNK1, exhibited temporal expression patterns during the FP5 stage, which inhibited the development time needed for the two almond cultivars. Cytokinin-type hormones presented stronger differential accumulation patterns between the flowering stages of the two almond cultivars. We cloned a pair of PdSVP and PdAGL15 genes that interact in the nucleus and may regulate the developmental progress of the two cultivars during the bud stage. Finally, we integrated several key findings to construct a flowchart depicting the delayed flowering development of almond cultivars. Changes in environmental conditions significantly influence the delayed flowering of Nonpareil almond. This study employed multiomics strategies to reveal the complex differential molecular mechanisms of flowering development in two almond cultivars, providing a reference for the subsequent breeding of high-quality late-flowering almond cultivars in Xinjiang.

NAC25 transcription factor regulates the degeneration of cytoplasmic membrane integrity and starch biosynthesis in rice endosperm through interacting with MADS29

Introduction

Grain filling is a crucial stage of the rice endosperm development. During this process, the endosperm accumulates abundant storage products such as starch and proteins, which determine both the yield and quality of the grain.

Methods

Here, we analyzed the expression of NAC25 transcription factor via qRT-PCR and histochemical GUS assays, and obtained its mutants by CRISPR/Cas9-based gene editing in ZH11.

Results and discussion

The results showed that NAC25 was expressed specifically in developing rice endosperm, and knockout of NAC25 led to delayed degeneration of cytoplasmic membrane integrity, reduced starch accumulation and chalky starchy endosperm. We showed that NAC25 interacted with MADS29, a MADS family transcription factor whose mutant also showed defective grain filling. These results provide novel insight into the transcriptional regulation of rice grain filling.

Genome-Wide Identification of the NAC Gene Family in Brassica rapa (L.) and Expression Pattern Analysis of BrNAC2s

Flowers are one of the most important organs in plants. Their development serves as a key indicator of the transition from vegetative to reproductive growth and is regulated by various internal signals and environmental factors. NAC (NAM, ATAF, CUC) transcription factors (TFs) play a crucial regulatory role in floral organ development; however, research on the analysis and identification of the NAC TF family in Chinese cabbage (Brassica rapa L.) remains limited. In this study, we performed a comprehensive genome-wide analysis of NACs in B. rapa and identified 279 members of the BrNAC gene family. Their physicochemical properties, domain structure, collinearity relation, and cis-regulatory elements were evaluated. Phylogenetic analysis indicates that NAC proteins from Arabidopsis, B. rapa, B. oleracea, and B. nigra can be classified into seven distinct clades. BrNACs exhibit a tissue-specific expression, and nine BrNACs being specifically expressed in the inflorescence. Furthermore, nine flower-related BrNACs were selected for RT-qPCR analysis to validate their expression profiles. BrNAC2s has been cloned to investigate their subcellular localization, and examine the expression patterns of their promoters in Arabidopsis inflorescences. BrNAC2a and BrNAC2c are highly expressed in stamens while BrNAC2b exhibits elevated expression in pistils and pedicel. Collectively, our findings enhance the understanding of the BrNAC family and provide a foundation for future studies on the molecular mechanisms of BrNACs in floral development.

PhNH10 Suppresses Low Temperature Tolerance in Petunia Through the Abscisic Acid-Dependent Pathway

Low-temperature stress limits plant growth, and reduces aesthetics of many ornamental plants. Plants have developed different adaptive mechanisms to cope with low-temperature stress, in which NAC transcription factor family members playing an important role in low-temperature tolerance. However, their roles in petunia in response to low temperature are still largely unknown. Here, we found that a NAC transcription factor, namely, PhNH10, negatively regulates low-temperature response in petunia. PhNH10-silenced and -CRISPR/Cas9 mutant plants displayed higher survival rate, anthocyanin content and abscisic acid concentration than PhNH10-overexpression and wild-type plants under low-temperature condition. PhNH10 can directly bind to the PhABA8ox promoter to active its expression, which further promotes the abscisic acid catabolism, while silencing of PhABA8ox increased the ABA concentration and low-temperature tolerance. In addition, PhNH10 interact with a low-temperature-related E2 ubiquitin-conjugating enzyme, PhUBC2-1, which in turn inhibited the binding capacity of PhNH10 on PhABA8ox promoter. Our research has elucidated an extensive mechanistic network underlying the PhNH10-mediated regulation of low-temperature response in petunia. This finding not only presents a new viewpoint in understanding the low-temperature tolerance mechanisms but also delineates a promising pathway for transgenic petunia with improved low-temperature resistance.

The LbNAM2-LbZDS module enhances drought resistance in wolfberry (Lycium barbarum) by participating in ABA biosynthesis

Wolfberry (Lycium barbarum L.) fruit, renowned for its high carotenoid content, is extensively used in traditional Chinese herbal medicine and cuisine. Drought is a significant global challenge to crop production, with carotenoids playing crucial roles in enhancing drought resistance in higher plants. ζ-Carotene desaturase (ZDS), a key enzyme in the carotenoid biosynthesis pathway, catalyzes the conversion of ζ-carotene to lycopene. However, the molecular mechanisms by which LbZDS responds to drought stress remain largely unexplored. In this study, we demonstrated that LbZDS transcription is induced by PEG, NaCl, and abscisic acid (ABA) treatments. Overexpression of LbZDS in both wolfberry and tomato plants conferred enhanced drought tolerance by promoting ABA synthesis. We further identified that the NAC transcription factor LbNAM2 directly binds to the promoter region of LbZDS and activates its expression, as evidenced by electrophoretic mobility shift assays, yeast one-hybrid assays, and dual-luciferase assays. Silencing LbNAM2, or dual silencing of LbNAM2 and LbZDS via virus-induced gene silencing (VIGS), severely compromised drought tolerance in wolfberry plants. Additionally, overexpression of LbZDS resulted in a marked increase in carotenoid content, while silencing either LbZDS, LbNAM2, or both together led to reduced carotenoid levels. In conclusion, our study provides critical insights into the functional roles and regulatory mechanisms of the LbNAM2-LbZDS module in drought stress response and carotenoid biosynthesis in wolfberry.

Multiple roles of NAC transcription factors in plant development and stress responses

NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) are a family of plant-specific TFs that play crucial roles in various aspects of plant development and stress responses. Here, we provide an in-depth review of the structural characteristics, regulatory mechanisms, and functional roles of NACs in different plant species. One of the key features of NACs is their ability to regulate gene expression through a variety of mechanisms, including binding to DNA sequences in the promoter regions of target genes, interacting with other TFs, and modulating chromatin structure. We discuss these mechanisms in detail, providing insights into the complex regulatory networks that govern the activity of NACs. We explore the diverse functions of these TFs in plant growth and development processes, including embryogenesis, seed development, root and shoot development, floral development and fruit ripening, secondary cell wall formation, and senescence. We also discuss the diverse regulatory roles of NACs in response to various stresses, including drought, flooding, heat, cold, salinity, nutrient deficit, and diseases. Lastly, we emphasize the crosstalk role of NACs between developmental processes and stress responses. This integrated perspective highlights how NACs orchestrate plant growth and resilience. Overall, this review provides a comprehensive overview of the pivotal roles of NACs in plant development and stress responses, emphasizing their potential for engineering stress-resistant crops and enhancing agricultural productivity.

Transcriptome‑wide excavation and expression pattern analysis of the NAC transcription factors in methyl jasmonate- and sodium chloride-induced Glycyrrhiza uralensis

The NAC family is among the most extensive sets of plant-exclusive transcription factors (TFs), which are crucial for various plant development and stress response processes. Although a growing number of studies have been carried out on the NAC family in different species, it has not been characterized in Glycyrrhiza uralensis. To thoroughly understand the effects of methyl jasmonate (MeJA) and sodium chloride (NaCl) inductions on NAC TFs and investigate the underlying regulatory mechanism of NAC TFs in response to MeJA and NaCl on the biosynthesis of metabolites, we used transcriptome sequencing combined with qRT‒PCR to explore differential gene expression. Comparative transcriptomic profiling by RNA sequencing (RNA-seq) revealed differentially expressed NAC TFs between MeJA/CK (Mock Control) and NaCl/CK. KEGG pathway analysis revealed that NAC TFs involved in starch and sucrose, carbohydrate, lipid, and amino acid metabolism, as well as terpenoid, polyketide, and flavonoid pathways, can regulate the MeJA- and NaCl-induced responses of G. uralensis. This research lays the groundwork for a thorough comprehension of the regulatory mechanism of NAC TFs in response to MeJA and NaCl induction and their involvement in the accumulation of secondary metabolites, which can provide a scientific basis for the cultivation of high-quality varieties of G. uralensis.

PcNAC25, a NAC transcription factor of Pugionium cornutum(L.) Gaertn conferring enhanced drought and salt stress tolerances in Arabidopsis

Pugionium cornutum (L.) Gaertn (P. cornutum) has strong tolerance to drought, salt and disease, but the tolerance mechanisms for such stresses in P. cornutum are largely unknown. In this study, we identified the PcNAC25 transcription factor gene in P. cornutum. Its open reading frame was revealed to comprise 891 bp, encoding a protein consisting of 297 amino acids, with an isoelectric point of 6.61. Phylogenetic analysis showed that PcNAC25 was most closely related to ANAC019. The expression of PcNAC25 was induced by dehydration, mannitol, heat, cold, salt stresses and abscisic acid (ABA), salicylic acid (SA), and methyl jasmonate (JA) treatments. A subcellular localization analysis confirmed that PcNAC25 was localized in the nucleus. The overexpressing PcNAC25 lines in Arabidopsis had longer roots than wild-type (WT) lines under drought and salt stress. The overexpression of PcNAC25 improved drought and salt tolerance in transgenic Arabidopsis. Under drought and salt stress, PcNAC25 transgenic lines exhibited higher the CAT, POD and SOD activities and scavenging ability of hydroxyl radical than WT, more proline accumulation than WT and less MDA and H2O2 content and superoxide anion production rate than WT. PcNAC25 transgenic lines also exhibited greater reduced water loss rate of detached leaves than WT. Meanwhile, DAB and NBT staining showed that the accumulation of hydrogen peroxide and superoxide anion in PcNAC25 transgenic lines were also less than WT. In addition, overexpressing PcNAC25 enhanced the expression of drought response genes (DREB2A, SOD4, RD29A, NCED3, POD3, P5CS1, PYR1 and SAG13) and salt response genes NHX, SLAH1, SOS1 and NPF6.3. The mentioned above results indicated that PcNAC25 is a positive regulator that activates ROS-scavenging enzymes and enhances root formation in Arabidopsis, which provided a basis for further research on the molecular mechanism of PCNAC25-mediated regulation of drought and salt stress, and also provided gene resources of drought and salt tolerance.

NAC transcription factors transcriptionally fine-tune signal homeostasis in plant systemic acquired resistance

Small signalling molecules, such as salicylic acid (SA) and N-hydroxypipecolic acid (NHP), act synergistically to activate systemic acquired resistance (SAR), a major form of plant inducible immunity. The transcriptional regulation of SA biosynthesis controlled by different transcription factors (TFs) has been well documented in SAR. Several TFs, e.g., SARD1, CBP60g and WRKY33, positively regulate NHP biosynthesis; however, direct negative modulators have remained elusive. Recently, Cai et al. (2024) identified a NAC triad composed of NAC-type TFs, NAC90, NAC36, and NAC61, that negatively regulates NHP and SA biosynthesis. NAC90 and NAC36 act as negative regulators of plant immunity by repressing transcription of ALD1, FMO1, and ICS1, the major NHP and SA biosynthetic genes, via direct binding to their promoters. These TFs, along with another NAC TF, NAC61, form heterodimers, further enhancing their repressive effects on NHP and SA biosynthesis. These findings establish the NAC90-NAC61-NAC36 triad as a negative regulator of NHP and SA levels. In this viewpoint article, we present our perspectives on further investigations to gain comprehensive insight into transcriptional regulation of SAR signal homeostasis.

Natural variation in MdNAC5 contributes to fruit firmness and ripening divergence in apple

Fruit firmness is an important trait for characterizing the quality and value of apple. It also serves as an indicator of fruit maturity, as it is a complex trait regulated by multiple genes. Resequencing techniques can be employed to elucidate variations in such complex fruit traits. Here, the whole genomes of 294 F 1 hybrids of 'Fuji' and 'Cripp's Pink' were resequenced, and a high-density binmap was constructed using 5014 bin markers with a total map distance of 2213.23 cM and an average map distance of 0.44 cM. Quantitative trait loci (QTLs) of traits related to fruit were mapped, and an A-T allele variant identified in the coding region of MdNAC5 was found to potentially regulate fruit firmness and ripening. The overexpression of MdNAC5 A resulted in higher production of methionine and 1-aminocyclopropanecarboxylic acid compared to MdNAC5 T , leading to reduced fruit firmness and accelerated ripening in apples and tomatoes. Furthermore, the activities of MdNAC5 A and MdNAC5 T were enhanced through their differential binding to the promoter regions of MdACS1 and MdERF3. Spatial variations in MdNAC5 A and MdNAC5 T caused changes in MdACS1 expression following their interaction with MdERF3. Ultimately, utilizing different MdNAC5 alleles offers a strategy to manipulate fruit firmness in apple breeding.

LncRNA81246 regulates resistance against tea leaf spot by interrupting the miR164d-mediated degradation of NAC1

Non-coding RNAs play crucial roles in plant responses to viral stresses. However, their molecular mechanisms in tea leaf spot responses remain unclear. In this study, using Camellia sinensis, we identified lncRNA81246 as a long non-coding RNA that localizes to both the nucleus and cytoplasm. It functions as a competitive endogenous RNA, thereby disrupting CsNAC1 (encoding NAC domain-containing protein 1) degradation mediated by miR164d. Silencing lncRNA81246 increased the resistance of tea plants to presistanceathogens, whereas transient lncRNA81246-overexpression plants showed decreased resistance to pathogens. Co-expression assays in Nicotiana benthamiana revealed that lncRNA81246 affects the miR164d-CsNAC1 regulatory module. Transient miR164d-overexpression and silencing assays demonstrated its positive regulation of tea plant resistance. Specifically, silencing its target, CsNAC1, enhanced disease resistance, whereas transient overexpression reduced plant resistance. Yeast one-hybrid, dual-luciferase, and RT-qPCR assay results suggested that CsNAC1 alters the expression of CsEXLB1, whereas AsODN and tobacco transient overexpression assays showed that CsEXLB1 negatively regulated tea plant resistance. Thus, our research demonstrated that lncRNA81246 acts as a mediator to interfere with the miR164d-CsNAC1 regulatory module involved in the disease resistance of tea plants.

PagNAC2a promotes phloem fiber development by regulating PagATL2 in poplar

Phloem fiber is a key component of phloem tissue and is involved in supporting its structural integrity. NAC domain transcription factors are master switches that regulate secondary cell wall (SCW) biosynthesis in xylem fibers, but the mechanism by which NACs regulate phloem fiber development remains unexplored. Here, a NAC2-like gene in poplar, PagNAC2a, was shown to be involved in phloem fiber differentiation. qRT-PCR and GUS staining revealed that PagNAC2a was specifically expressed in the phloem zone of poplar stems. The overexpression of PagNAC2a in poplar increased plant biomass by increasing plant height, stem diameter, and leaf area. Stem anatomy analysis revealed that overexpression of PagNAC2a resulted in enhanced phloem fiber differentiation and cell wall deposition. In addition, PagNAC2a directly upregulated the expression of PagATL2, a gene involved in phloem development, as revealed by yeast one hybrid (Y1H) and electrophoretic mobility shift assay (EMSA) assays. Overall, we proposed that the PagNAC2a was a positive regulator of phloem fiber development in poplar, and these results provided insights into the molecular mechanisms involved in the differentiation of phloem fibers.

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.

VvRF2b interacts with VvTOR and influences VvTOR-regulated sugar metabolism in grape

The production of top-quality wines is closely related to the quality of the wine grapes. In wine grapes (Vitis vinifera L., Vv), sugar is a crucial determinant of berry quality, regulated by an interplay of various transcription factors and key kinases. Many transcription factors involved in sugar metabolism remain unexplored. Target of Rapamycin (TOR) is an important protein kinase in plants, recently found to regulate sugar metabolism in grapes. However, transcription factors or other factors involved in this process are rarely reported. Here, we utilized transgenic callus tissues from 'Cabernet Sauvignon' grape fruit engineered via gene overexpression (oe) and CRISPR/Cas9-based gene knockout (ko), and discovered a bZIP transcription factor, VvRF2b, whose knockout resulted in increased accumulation of fructose and sucrose, indicating that VvRF2b is a negative regulator of sugar accumulation. Subcellular localization and transcriptional activation tests showed that VvRF2b is an activator of transcription located both in the nucleus and cell membrane. Analysis of VvRF2b and VvTOR gene levels and sugar contents (glucose, fructose, and sucrose) in 'Cabernet Sauvignon' grape fruits at 30, 70, and 90 days after bloom (DAB) revealed that VvRF2b is expressed more highly during fruit development, while VvTOR is expressed more during the sugar accumulation phase, furthermore, VvTOR gene levels in koVvRF2b transgenic calli increased significantly, suggesting a strong relationship between the knockout of VvRF2b and the overexpression of VvTOR. Additionally, bimolecular fluorescence complementation and luciferase complementation assays demonstrated the interaction between VvRF2b and VvTOR proteins. After knocking out the VvRF2b gene in oeVvTOR calli, it was found that the knockout of VvRF2b promotes VvTOR-regulated sucrose accumulation and enhances the expression of sugar metabolism-related genes regulated by VvTOR. In summary, our results suggest that VvRF2b interacts with VvTOR protein and influences VvTOR-regulated sugar metabolism.

Lysine 98 in NAC20/NAC26 transcription factors: a key regulator of starch and protein synthesis in rice endosperm

Starch and proteins are main storage product to determine the appearance, cooking, texture, and nutritional quality of rice (Oryza sativa L.). OsNAC20 and OsNAC26, as pivotal transcription factors, redundantly regulate the expression of genes responsible for starch and protein synthesis in the rice endosperm. Any knockout of OsNAC20 or OsNAC26 did not result in visible endosperm defects. In this study, we had isolated and characterized a mutant named as floury endosperm25 (flo25). The caryopsis of the flo25 mutant exhibits a floury endosperm, accompanied by reductions in both the 1000-grain weight and grain length, as well as diminished levels of total starch and protein. Through map-based cloning, it was determined that FLO25 encodes a NAM, ATAF, and CUC (NAC) transcription factors, namely OsNAC26, with a lysine to asparagine substitution at position 98 in the flo25 mutant. Remarkably, lysine 98 is conserved across plants species, and this mutation does not alter the subcellular localization of OsNAC26 but significantly attenuates its transcriptional activity and its ability to activate downstream target genes. Furthermore, the mutant protein encoded by OsNAC26-flo25 could interact with OsNAC20, disrupting the native interaction between OsNAC20 proteins. Additionally, when lysine 98 is substituted with asparagine in OsNAC20, the resulting mutant protein, OsNAC20(K98N), similarly disrupts the interaction between OsNAC26 proteins. Collectively, these findings underscore the pivotal role of Lysine 98 (K) in modulating the transcriptional activity of NAC20/NAC26 within the rice endosperm.

Genome-Wide Analysis of CSL Family Genes Involved in Petiole Elongation, Floral Petalization, and Response to Salinity Stress in Nelumbo nucifera

Lotus (Nelumbo nucifera), a perennial aquatic plant, endures various environmental stresses. Its diverse ornamental traits make it an ideal model for studying multigene family functional differentiation and abiotic stress responses. The cellulose synthase-like (CSL) gene family includes multiple subfamilies and holds potentially pivotal roles in plant growth, development, and stress responses. Thus, understanding this family is essential for uncovering the attributes of ancient dicotyledonous lotus species and offering new genetic resources for targeted genetic improvement. Herein, we conducted a genome-wide NnCSL gene identification study, integrating tissue-specific expression analysis, RNA-seq, and qRT-PCR validation. We identified candidate NnCSL genes linked to petiole elongation, floral petalization, salinity stress responses, and potential co-expressed TFs. 22 NnCSL genes were categorized into six subfamilies: NnCSLA, NnCSLB, NnCSLC, NnCSLD, NnCSLE, and NnCSLG. Promoter regions contain numerous cis-acting elements related to growth, development, stress responses, and hormone regulation. Nineteen NnCSL genes showed specific differential expression in LPA (large plant architecture) versus SPA (small plant architecture): petioles, petalized carpels (CP) and normal carpels (C), and petalized stamens (SP) and normal stamens (S). Notably, most NnCSLC, NnCSLA, and NnCSLB subfamily genes play diverse roles in various aspects of lotus growth and development, while NnCSLE and NnCSLG are specifically involved in carpel petalization and petiole elongation, respectively. Additionally, 11 candidate NnCSL genes responsive to salinity stress were identified, generally exhibiting antagonistic effects on growth and developmental processes. These findings provide an important theoretical foundation and novel insights for the functional study of NnCSL genes in growth, development, and stress resistance in lotus.

LkERF6 enhances drought and salt tolerance in transgenic tobacco by regulating ROS homeostasis

The transcription factor Ethylene Responsive Factor (ERF) is crucial for responding to various environmental stressors. Proteins containing the ERF-associated amphiphilic repression (EAR) motif often inhibit gene expression. However, the functions of LkERF, an EAR motif-containing protein from Larix kaempferi, especially in reactive oxygen species (ROS) homeostasis, are not well understood. In the present research, we introduce a novel transcription factor, LkERF6, which contains an EAR motif and positively regulates gene expression, thereby enhancing drought and salt tolerance in tobacco. LkERF6 is classified within the ERF-B1 subfamily due to its conserved AP2/ERF domain and EAR motif. Subcellular localization assays demonstrated LkERF6 is primarily localized in the nucleus. Further analysis revealed that LkERF6 interacts with GCC and DRE elements and is significantly induced by NaCl and PEG6000. Moreover, LkERF6 transgenic tobacco plants exhibit lower ROS accumulation and higher levels of antioxidant enzyme activities. Additionally, correlation analysis identified a strong association between LkERF6 and three genes: LkSOD, LkCCS, and LkCAT. Y1H, EMAS, and DLR assays confirmed that LkERF6 directly interacts with the promoters of these genes through GCC-box and DRE-box to activate their expression. These findings shed new light on the function of EAR motif-containing transcription factors and highlight LkERF6's crucial role in enhancing abiotic stress resistance by activating multiple ROS clearance genes.

Genome-wide identification of the NAC family in Hemerocallis citrina and functional analysis of HcNAC35 in response to abiotic stress in watermelon

Introduction

NAC (NAM, ATAF, and CUC) transcription factor family, one of the important switches of transcription networks in plants, functions in plant growth, development, and stress resistance. Night lily (Hemerocallis citrina) is an important horticultural perennial monocot plant that has edible, medicinal, and ornamental values. However, the NAC gene family of night lily has not yet been analyzed systematically to date.

Methods

Therefore, we conducted a genome-wide study of the HcNAC gene family and identified a total of 113 HcNAC members from the Hemerocallis citrina genome.

Results

We found that 113 HcNAC genes were unevenly distributed on 11 chromosomes. Phylogenetic analysis showed that they could be categorized into 16 instinct subgroups. Proteins clustering together exhibited similar conserved motifs and intron-exon structures. Collinearity analysis indicated that segmental and tandem duplication might contribute to the great expansion of the NAC gene family in night lily, whose relationship was closer with rice than Arabidopsis. Additionally, tissue-specific pattern analysis indicated that most HcNAC genes had relatively higher expression abundances in roots. RNA-Seq along with RT-qPCR results jointly showed HcNAC genes expressed differently under drought and salinity stresses. Interestingly, HcNAC35 was overexpressed in watermelon, and the stress resilience of transgenic lines was much higher than that of wild-type watermelon, which revealed its wide participation in abiotic stress response.

Conclusion

In conclusion, our findings provide a new prospect for investigating the biological roles of NAC genes in night lily.

Integrative Analysis of Transcriptome and Metabolome Reveals the Pivotal Role of the NAM Family Genes in Oncidium hybridum Lodd. Pseudobulb Growth

Oncidium hybridum Lodd. is an important ornamental flower that is used as both a cut flower and a potted plant around the world; additionally, its pseudobulbs serve as essential carriers for floral organs and flower development. The NAM gene family is crucial for managing responses to various stresses as well as regulating growth in plants. However, the mechanisms by which NAM genes regulate the development of pseudobulbs remain unclear. In this study, a total of 144 NAM genes harboring complete structural domains were identified in O. hybridum. The 144 NAM genes were systematically classified into 14 distinct subfamilies via phylogenetic analysis. Delving deeper into the conserved motifs revealed that motifs 1-6 exhibited remarkable conservation, while motifs 7-10 presented in a few NAM genes only. Notably, NAM genes sharing identical specific motifs were classified into the same subfamily, indicating functional relatedness. Furthermore, the examination of occurrences of gene duplication indicated that the NAM genes display 16 pairs of tandem duplications along with five pairs of segmental duplications, suggesting their role in genetic diversity and potential adaptive evolution. By conducting a correlation analysis integrating transcriptomics and metabolomics at four stages of pseudobulb development, we found that OhNAM023, OhNAM030, OhNAM007, OhNAM019, OhNAM083, OhNAM047, OhNAM089, and OhNAM025 exhibited significant relationships with the endogenous plant hormones jasmonates (JAs), hinting at their potential involvement in hormonal signaling. Additionally, OhNAM089, OhNAM025, OhNAM119, OhNAM055, and OhNAM136 showed strong links with abscisic acid (ABA) and abscisic acid glucose ester (ABA-GE), suggesting the possible regulatory function of these NAM genes in plant growth and stress responses. The 144 NAM genes identified in this study provide a basis for subsequent research and contribute to elucidating the intricate molecular mechanisms of NAM genes in Oncidium and potentially in other species.

Loss of OsSPL8 Function Confers Improved Resistance to Glufosinate and Abiotic Stresses in Rice

Weeds are among the most significant factors contributing to decreases in crop yield and quality. Glufosinate, a nonselective, broad-spectrum herbicide, has been extensively utilized for weed control in recent decades. However, crops are usually sensitive to glufosinate. Therefore, the development of glufosinate-resistant crops is crucial for effective weed management in agriculture. In this study, we characterized a SQUAMOSA promoter-binding-like (SPL) factor, OsSPL8, which acts as a negative regulator of glufosinate resistance by inhibiting the transcription of OsGS1;1 and OsGS2 and consequently reducing GS activity. Furthermore, the loss of OsSPL8 function enhanced tolerance to drought and salt stresses. Transcriptomic comparisons between the gar18-3 mutant and wild type revealed that OsSPL8 largely downregulates stress-responsive genes and upregulates growth-related genes. We demonstrated that OsSPL8 directly regulates OsOMTN6 and OsNAC17, which influence drought tolerance. In addition, OsSPL8 directly represses the expression of salt stress tolerance-related genes such as OsHKT1.1 and OsTPP1. Collectively, our results demonstrate that OsSPL8 is a negative regulator of both glufosinate resistance and abiotic stress tolerance.

MdSINA2-MdNAC104 Module Regulates Apple Alkaline Resistance by Affecting γ-Aminobutyric Acid Synthesis and Transport

Soil alkalization is an adverse factor limiting plant growth and yield. As a signaling molecule and secondary metabolite, γ-aminobutyric acid (GABA) responds rapidly to alkaline stress and enhances the alkaline resistance of plants. However, the molecular mechanisms by which the GABA pathway adapts to alkaline stress remain unclear. In this study, a transcription factor, MdNAC104 is identified, from the transcriptome of the alkaline-stressed roots of apple, which effectively reduces GABA levels and negatively regulates alkaline resistance. Nevertheless, applying exogenous GABA compensates the negative regulatory mechanism of overexpressed MdNAC104 on alkaline resistance. Further research confirms that MdNAC104 repressed the GABA biosynthetic gene MdGAD1/3 and the GABA transporter gene MdALMT13 by binding to their promoters. Here, MdGAD1/3 actively regulates alkaline resistance by increasing GABA synthesis, while MdALMT13 promotes GABA accumulation and efflux in roots, resulting in an improved resistance to alkaline stress. This subsequent assays reveal that MdSINA2 interacts with MdNAC104 and positively regulates root GABA content and alkaline resistance by ubiquitinating and degrading MdNAC104 via the 26S proteasome pathway. Thus, the study reveals the regulation of alkaline resistance and GABA homeostasis via the MdSINA2-MdNAC104-MdGAD1/3/MdALMT13 module in apple. These findings provide novel insight into the molecular mechanisms of alkaline resistance in plants.

Pathogen resistance was negatively regulated by the NAC transcription factor ScATAF1 in sugarcane

The NAC (NAM, ATAF, and CUC) is one of the largest transcription factor gene families in plants. In this study, 180, 141, and 131 NAC family members were identified from Saccharum complex, including S. officinarum, S. spontaneum, and Erianthus rufipilus. The Ka/Ks ratio of ATAF subfamily was all less than 1. Besides, 52 ATAF members from 12 representative plants were divided into three clades and there was only a significant expansion in maize. Surprisingly, ABA and JA cis-elements were abundant in hormonal response factor, followed by transcriptional regulator and abiotic stressor. The ATAF subfamily was differentially expressed in various tissues, under low temperature and smut pathogen treatments. Further, the ScATAF1 gene, with high expression in leaves, stem epidermis, and buds, was isolated. The encoded protein, lack of self-activation activity, was situated in the cell nucleus. Moreover, SA and JA stresses down-regulated the expression of this gene, while ABA, NaCl, and 4°C treatments led to its up-regulation. Interestingly, its expression in the smut susceptible sugarcane cultivars was much higher than the smut resistant ones. Notably, the colors presented slight brown in tobacco transiently overexpressing ScATAF1 at 1 d after DAB staining, while the symptoms were more obvious at 3 d after inoculation with Ralstonia solanacearum, with ROS, JA, and SA signaling pathway genes significantly up-regulated. We thus speculated ScATAF1 gene could negatively mediate hypersensitive reactions and produce ROS by JA and SA signaling pathways. These findings lay the groundwork for in-depth investigation on the biological roles of ATAF subfamily in sugarcane.

NAC transcription factor ATAF1 negatively modulates the PIF-regulated hypocotyl elongation under a short-day photoperiod

Day length modulates hypocotyl elongation in seedlings to optimize their overall fitness. Variations in cell growth-associated genes are regulated by several transcription factors. However, the specific transcription factors through which the plant clock increases plant fitness are still being elucidated. In this study, we identified the no apical meristem, Arabidopsis thaliana-activating factor (ATAF-1/2), and cup-shaped cotyledon (NAC) family transcription factor ATAF1 as a novel repressor of hypocotyl elongation under a short-day (SD) photoperiod. Variations in day length profoundly affected the transcriptional and protein levels of ATAF1. ATAF1-deficient mutant exhibited increased hypocotyl length and cell growth-promoting gene expression under SD conditions. Moreover, ATAF1 directly targeted and repressed the expression of the cycling Dof factor 1/5 (CDF1/5), two key transcription factors involved in hypocotyl elongation under SD conditions. Additionally, ATAF1 interacted with and negatively modulated the effects of phytochrome-interacting factor (PIF), thus inhibiting PIF-promoted gene expression and hypocotyl elongation. Taken together, our results revealed ATAF1-PIF as a crucial pair modulating the expression of key transcription factors to facilitate plant growth during day/night cycles under fluctuating light conditions.

Genome-wide investigation and analysis of NAC transcription factor family in Populus tomentosa and expression analysis under salt stress

The NAC transcription factor family is one of the largest families of TFs in plants, and members of NAC gene family play important roles in plant growth and stress response. Recent release of the haplotype-resolved genome assembly of P. tomentosa provide a platform for NAC protein genome-wide analysis. A total of 270 NAC genes were identified and a comprehensive overview of the PtoNAC gene family is presented, including gene promoter, structure and conserved motif analyses, chromosome localization and collinearity analysis, protein phylogeny, expression pattern, and interaction analysis. The results indicate that protein length, molecular weight, and theoretical isoelectric points of the NAC TF family vary, while gene structure and motif are relatively conserved. Chromosome mapping analysis showed that the P. tomentosa NAC genes are unevenly distributed on 19 chromosomes. The interchromosomal evolutionary results indicate 12 pairs of tandem and 280 segmental duplications. Segmental duplication is possibly related to amplification of P. tomentosa NAC gene family. Expression patterns of 35 PtoNAC genes from P. tomentosa subgroup were analysed under high salinity, and seven NAC genes were induced by this treatment. Promoter and protein interaction network analyses showed that PtoNAC genes are closely associated with growth, development, and abiotic and biotic stress, especially salt stress. These results provide a meaningful reference for follow-up studies of the functional characteristics of NAC genes in the mechanism of stress response and their potential roles in development of P. tomentosa.

Transcription factor PgNAC72 activates DAMMARENEDIOL SYNTHASE expression to promote ginseng saponin biosynthesis

Ginsenosides, the primary bioactive constituents in ginseng (Panax ginseng), possess substantial pharmacological potential and are in high demand in the market. The plant hormone methyl jasmonate (MeJA) effectively elicits ginsenoside biosynthesis in P. ginseng, though the regulatory mechanism remains largely unexplored. NAC transcription factors are critical in intricate plant regulatory networks and participate in numerous plant physiological activities. In this study, we identified a MeJA-responsive NAC transcription factor gene, PgNAC72, from a transcriptome library produced from MeJA-treated P. ginseng callus. Predominantly expressed in P. ginseng flowers, PgNAC72 localizes to the nucleus. Overexpressing PgNAC72 (OE-PgNAC72) in P. ginseng callus notably elevated total saponin levels, particularly dammarane-type ginsenosides, by upregulating dammarenediol synthase (PgDDS), encoding a key enzyme in the ginsenoside biosynthesis pathway. Electrophoretic mobility shift assays and dual-luciferase assays confirmed that PgNAC72 binds to the NAC-binding elements in the PgDDS promoter, thereby activating its transcription. Further RNA-seq and terpenoid metabolomic data in the OE-PgNAC72 line confirmed that PgNAC72 enhances ginsenoside biosynthesis. These findings uncover a regulatory role of PgNAC72 in MeJA-mediated ginsenoside biosynthesis, providing insights into the ginsenoside regulatory network and presenting a valuable target gene for metabolic engineering.

Mechanistic analysis of the hardening process of the thorns on stems of Bougainvillea glabra "Elizabeth Angus"

Introduction: Bougainvillea glabra "Elizabeth Angus" is a thorny woody vine or shrub. However, the hard thorns are considered a deficiency in its ornamental value. Methods: To find the genes and pathways related to the hardening process of the thorns on the stems of B. glabra, the eukaryotic unreferenced transcriptome sequencing analysis was conducted to explore the 3 stages of the thorn-hardening process. Total RNA was extracted from thorns and stems, and transcriptome libraries were constructed and sequenced using unreferenced Illumina sequencing. Results: Gene function annotation was performed using various databases, resulting in 8937 co-annotated genes. The density distribution of Fragments Per Kilobase of transcript per Million mapped reads (FPKM) depicted the overall gene expression patterns. The study found that stage 2 as the period of highest gene expression activity during the thorns hardening process in B. glabra. Differential expression analysis revealed that during thorn-hardening, 1045 genes up-regulated and 391 genes down-regulated significantly in thorns at stage 2 compared to stage 1 (early stage of thorns formation). Meanwhile, 938 genes up-regulated and 784 genes down-regulated significantly in stems. At stage 3, as thorns became harder, 63 genes exhibited notable expression increase and 98 genes' expression decreased obviously within thorns, and 46 genes up-regulated and 29 genes down-regulated in stems, compared to stage 2. Phenylpropanoid biosynthesis was the key step in the hardening process of the thorns of B. glabra. The formation and hardening of thorns on the stem of B. glabra was a process in which lignin gradually accumulated in the thorns, and several genes were involved in this process. They include PAL (EC:4.3.1.24), CYP73A (EC:1.14.14.91), 4CL (EC:6.2.1.12), CCR (EC:1.2.1.44), CAD (EC:1.1.1.195) and POX (EC:1.11.1.7). Discussion: This transcriptome analysis offers insights into the molecular mechanisms underlying thorns development in this plant species.

MpNAC1, a transcription factor from the mangrove associate Millettia pinnata, confers salt and drought stress tolerance in transgenic Arabidopsis and rice

Pongamia (Millettia pinnata Syn. Pongamia pinnata), a mangrove associate plant, exhibits good stress tolerance, making it a treasure of genetic resources for crop improvement. NAC proteins are plant-specific transcription factors, which have been elucidated to participate in the regulation and tolerance of abiotic stresses (such as salt and drought). Here, we identified a salt-induced gene from Pongamia, MpNAC1, which encodes an NAC factor sharing five highly conserved domains with other NACs and exhibits close homology to AtNAC19/AtNAC55/AtNAC72 in Arabidopsis. MpNAC1 showed nuclear localization and transcriptional activator activity. MpNAC1-overexpressing Arabidopsis exhibited significantly stronger salt and drought tolerance compared with wild-type plants. The expression levels of stress-responsive genes were activated in transgenic Arabidopsis. Furthermore, the heterologous expression of MpNAC1 also enhanced the salt and drought tolerance of transgenic rice. The major agronomic traits, such as plant height and tiller number, panicle length, grain size, and yield, were similar between the transgenic lines and wild type under normal field growth conditions. RNA-Seq analysis revealed that MpNAC1 significantly up-regulated stress-responsive genes and activated the biosynthesis of secondary metabolites such as flavonoids, resulting in increased stress tolerance. Taken together, the MpNAC1 increased salt and drought stress tolerance in transgenic plants and did not retard the plant growth and development under normal growth conditions, suggesting the potential of MpNAC1 in breeding stress-resilient crops.

Genome-wide analysis of NAC transcription factors and exploration of candidate genes regulating selenium metabolism in Broussonetia papyrifera

MAIN CONCLUSION

Genome-wide identification revealed 79 BpNAC genes belonging to 16 subfamilies, and their gene structures and evolutionary relationships were characterized. Expression analysis highlighted their importance in plant selenium stress responses. Paper mulberry (Broussonetia papyrifera), a deciduous arboreal plant of the Moraceae family, is distinguished by its leaves, which are abundant in proteins, polysaccharides, and flavonoids, positioning it as a novel feedstock. NAC transcription factors, exclusive to plant species, are crucial in regulating growth, development, and response to biotic and abiotic stress. However, extensive characterization of the NAC family within paper mulberry is lacking. In this study, 79 BpNAC genes were identified from the paper mulberry genome, with an uneven distribution across 13 chromosomes. A comprehensive, genome-wide analysis of BpNACs was performed, including investigating gene structures, promoter regions, and chromosomal locations. Phylogenetic tree analysis, alongside comparisons with Arabidopsis thaliana NACs, allowed for categorizing these genes into 16 subfamilies in alignment with gene structure and motif conservation. Collinearity analysis suggested a significant homologous relationship between the NAC genes of paper mulberry and those in Morus notabilis, Ficus hispida, Antiaris toxicaria, and Cannabis sativa. Integrating transcriptome data and Se content revealed that 12 BpNAC genes were associated with selenium biosynthesis. Subsequent RT-qPCR analysis corroborated the correlation between BpNAC59, BpNAC62 with sodium selenate, and BpNAC55 with sodium selenite. Subcellular localization experiments revealed the nuclear functions of BpNAC59 and BpNAC62. This study highlights the potential BpNAC transcription factors involved in selenium metabolism, providing a foundation for strategically breeding selenium-fortified paper mulberry.

CcNAC6 Acts as a Positive Regulator of Secondary Cell Wall Synthesis in Sudan Grass (Sorghum sudanense S.)

The degree of forage lignification is a key factor affecting its digestibility by ruminants such as cattle and sheep. Sudan grass (Sorghum sudanense S.) is a high-quality sorghum forage, and its lignocellulose is mostly stored in the secondary cell wall. However, the secondary cell wall synthesis mechanism of Sudan grass has not yet been studied in depth. To further study the secondary cell wall synthesis mechanism of Sudan grass using established transcriptome data, this study found that CcNAC6, a homologous gene of Arabidopsis AtSND2, is related to the secondary cell wall synthesis of Sudan grass. Accordingly, we constructed a CcNAC6-overexpressing line of Arabidopsis to investigate the function of the CcNAC6 gene in secondary cell wall synthesis. The results showed that the overexpression of the CcNAC6 gene could significantly increase the lignin content of Arabidopsis. Based on subcellular localization analysis, CcNAC6 is found in the nucleus. In addition, yeast two-hybridization screening showed that CcCP1, associated with secondary cell wall synthesis, can interact with CcNAC6. Therefore, the above results indicate that CcNAC6 has a positive regulatory effect on the secondary cell wall synthesis of Sudan grass, and it is speculated that CcNAC6 may be the main regulator of the secondary cell wall synthesis of Sudan grass through its interaction with another regulatory protein, CcCP1. This study provides a theoretical basis and new genetic resources for the creation of new Sudan grass germplasm with a low lignin content.

Functional characterization of sugarcane ScFTIP1 reveals its role in Arabidopsis flowering

The timing of floral transition is essential for reproductive success in flowering plants. In sugarcane, flowering time affects the production of sugar and biomass. Although the function of the crucial floral pathway integrators, FLOWERING LOCUS T (FT), in sugarcane, has been uncovered, the proteins responsible for FT export and the underlying mechanism remain unexplored. In this study, we identified a member of the multiple C2 domain and transmembrane region proteins (MCTPs) family in sugarcane, FT-interacting protein 1 (ScFTIP1), which was localized to the endoplasmic reticulum. Ectopic expression of ScFTIP1 in the Arabidopsis mutant ftip1-1 rescued the late-flowering phenotype. ScFTIP1 interacted with AtFT in vitro and in vivo assays. Additionally, ScFTIP1 interacted with ScFT1 and the floral inducer ScFT3. Furthermore, we found that the NAC member, ScNAC23, could directly bind to the ScFTIP1 promoter and negatively regulate its transcription. Overall, our findings revealed the function of ScFTIP1 and proposed a potential mechanism underlying flowering regulation in sugarcane.

Picea wilsonii NAC31 and DREB2A Cooperatively Activate ERD1 to Modulate Drought Resistance in Transgenic Arabidopsis

The NAC family of transcription factors (TFs) regulate plant development and abiotic stress. However, the specific function and response mechanism of NAC TFs that increase drought resistance in Picea wilsonii remain largely unknown. In this study, we functionally characterized a member of the PwNAC family known as PwNAC31. PwNAC31 is a nuclear-localized protein with transcriptional activation activity and contains an NAC domain that shows extensive homology with ANAC072 in Arabidopsis. The expression level of PwNAC31 is significantly upregulated under drought and ABA treatments. The heterologous expression of PwNAC31 in atnac072 Arabidopsis mutants enhances the seed vigor and germination rates and restores the hypersensitive phenotype of atnac072 under drought stress, accompanied by the up-regulated expression of drought-responsive genes such as DREB2A (DEHYDRATION-RESPONSIVE ELEMENT BINDING PROTEIN 2A) and ERD1 (EARLY RESPONSIVE TO DEHYDRATION STRESS 1). Yeast two-hybrid and bimolecular fluorescence complementation assays confirmed that PwNAC31 interacts with DREB2A and ABF3 (ABSCISIC ACID-RESPONSIVE ELEMENT-BINDING FACTOR 3). Yeast one-hybrid and dual-luciferase assays showed that PwNAC31, together with its interaction protein DREB2A, directly regulated the expression of ERD1 by binding to the DRE element of the ERD1 promoter. Collectively, our study provides evidence that PwNAC31 activates ERD1 by interacting with DREB2A to enhance drought tolerance in transgenic Arabidopsis.

Characterization of NAC Gene Family in Ammopiptanthus mongolicus and Functional Analysis of AmNAC24, an Osmotic and Cold-Stress-Induced NAC Gene

The NAC family of transcription factors (TFs) is recognized as a significant group within the plant kingdom, contributing crucially to managing growth and development processes in plants, as well as to their response and adaptation to various environmental stressors. Ammopiptanthus mongolicus, a temperate evergreen shrub renowned for its remarkable resilience to low temperatures and drought stress, presents an ideal subject for investigating the potential involvement of NAC TFs in stress response mechanisms. Here, the structure, evolution, and expression profiles of NAC family TFs were analyzed systematically, and a cold and osmotic stress-induced member, AmNAC24, was selected and functionally characterized. A total of 86 NAC genes were identified in A. mongolicus, and these were divided into 15 groups. Up to 48 and 8 NAC genes were generated by segmental duplication and tandem duplication, respectively, indicating that segmental duplication is a predominant mechanism in the expansion of the NAC gene family in A. mongolicus. A considerable amount of NAC genes, including AmNAC24, exhibited upregulation in response to cold and osmotic stress. This observation is in line with the detection of numerous cis-acting elements linked to abiotic stress response in the promoters of A. mongolicus NAC genes. Subcellular localization revealed the nuclear residence of the AmNAC24 protein, coupled with demonstrable transcriptional activation activity. AmNAC24 overexpression enhanced the tolerance of cold and osmotic stresses in Arabidopsis thaliana, possibly by maintaining ROS homeostasis. The present study provided essential data for understanding the biological functions of NAC TFs in plants.

Supplementary Low Far-Red Light Promotes Proliferation and Photosynthetic Capacity of Blueberry In Vitro Plantlets

Far-red light exerts an important regulatory influence on plant growth and development. However, the mechanisms underlying far-red light regulation of morphogenesis and photosynthetic characteristics in blueberry plantlets in vitro have remained elusive. Here, physiological and transcriptomic analyses were conducted on blueberry plantlets in vitro supplemented with far-red light. The results indicated that supplementation with low far-red light, such as 6 μmol m-2 s-1 and 14 μmol m-2 s-1 far-red (6FR and 14FR) light treatments, significantly increased proliferation-related indicators, including shoot length, shoot number, gibberellin A3, and trans-zeatin riboside content. It was found that 6FR and 14 FR significantly reduced chlorophyll content in blueberry plantlets but enhanced electron transport rates. Weighted correlation network analysis (WGCNA) showed the enrichment of iron ion-related genes in modules associated with photosynthesis. Genes such as NAC, ABCG11, GASA1, and Erf74 were significantly enriched within the proliferation-related module. Taken together, we conclude that low far-red light can promote the proliferative capacity of blueberry plantlets in vitro by affecting hormone pathways and the formation of secondary cell walls, concurrently regulating chlorophyll content and iron ion homeostasis to affect photosynthetic capacity.

The Functions of an NAC Transcription Factor, GhNAC2-A06, in Cotton Response to Drought Stress

Drought stress imposes severe constraints on crop growth and yield. The NAC transcription factors (TF) play a pivotal role in regulating plant stress responses. However, the biological functions and regulatory mechanisms of many cotton NACs have not been explored. In this study, we report the cloning and characterization of GhNAC2-A06, a gene encoding a typical cotton NAC TF. The expression of GhNAC2-A06 was induced by PEG treatment, drought stress, and ABA treatment. Furthermore, we investigated its function using the virus-induced gene silencing (VIGS) method. GhNAC2-A06 silenced plants exhibited a poorer growth status under drought stress conditions compared to the controls. The GhNAC2-A06 silenced cotton plants had a lower leaf relative water and chlorophyll content and a higher MDA content compared to the controls under the drought treatment. The levels of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) enzyme activity in the GhNAC2-A06 silenced plants were found to be lower compared to the controls when exposed to drought stress. Additionally, the downregulation of the drought stress-related genes, GhSAP12-D07, GhNCED1-A01, GhLEA14-A11, GhZAT10-D02, GhPROT2-A05, GhABF3-A03, GhABF2-D05, GhSAP3-D07, and GhCPK1-D04, was observed in the GhNAC2-A06 silenced cotton. Together, our research reveals that GhNAC2-A06 plays a role in the reaction of cotton to drought stress by affecting the expression of genes related to drought stress. The data obtained from this study lay the theoretical foundation for further in-depth research on the biological function and regulatory mechanisms of GhNAC2-A06.