NAC103, a NAC family transcription factor, regulates ABA response during seed germination and seedling growth in Arabidopsis

Hallmarks of DNA Damage Response in Germination Across Model and Crop Species

DNA damage response (DDR) contributes to seed quality by guarding genome integrity in the delicate phases of pre- and post-germination. As a key determinant of stress tolerance and resilience, DDR has notable implications on the wider scale of the agroecosystems challenged by harsh climatic events. The present review focuses on the existing and documented links that interconnect DDR efficiency with an array of molecular hallmarks with biochemical, molecular, and physiological valence within the seed metabolic networks. The expression of genes encoding DDR sensors, transducers, mediators, and effectors is interpreted as a source of conserved hallmarks, along with markers of oxidative damage reflecting the seed's ability to germinate. Similarly, the accumulation patterns of proteins and metabolites that contribute to DNA stability are predictive of seed quality traits. While a list of candidates is presented from multiple models and crop species, their interaction with chromatin dynamics, cell cycle progression, and hormonal regulation provides further levels of analysis to investigate the seed stress response holistically. The identification of novel hallmarks of DDR in seeds constitutes a framework to prompt validation with different experimental systems, to refine the current models of pre-germinative metabolism, and to promote targeted approaches for seed quality evaluation.

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.

Genome-Wide Identification of NAC Family Genes in Oat and Functional Characterization of AsNAC109 in Abiotic Stress Tolerance

The plant-specific NAC gene family is one of the largest transcription factor families, participating in plant growth regulation and stress response. Despite extensive characterization in various plants, our knowledge of the NAC family in oat is lacking. Herein, we identified 333 NAC genes from the latest release of the common oat genome. We provide a comprehensive overview of the oat NAC gene family, covering gene structure, chromosomal localization, phylogenetic characteristics, conserved motif compositions, and gene duplications. AsNAC gene expression in different tissues and the response to various abiotic stresses were characterized using RT-qPCR. The main driver of oat NAC gene family expansion was identified as segmental duplication using collinearity analysis. In addition, the functions of AsNAC109 in regulating abiotic stress tolerance in Arabidopsis were clarified. This is the first genome-wide investigation of the NAC gene family in cultivated oat, which provided a unique resource for subsequent research to elucidate the mechanisms responsible for oat stress tolerance and provides valuable clues for the improvement of stress resistance in cultivated oat.

OsNAC3 regulates seed germination involving abscisic acid pathway and cell elongation in rice

Seed germination is a critical trait for the success of direct seeding in rice cultivation. However, the underlying mechanism determining seed germination is largely unknown in rice. Here, we report that NAC transcription factor OsNAC3 positively regulates seed germination of rice. OsNAC3 regulates seed germination involving abscisic acid (ABA) pathway and cell elongation. OsNAC3 can directly bind to the promoter of ABA catabolic gene OsABA8ox1 and cell expansion gene OsEXP4, which consequently activates their expressions during seed germination. We also find that the expression of OsEXP4 is reduced by ABA during seed germination in rice. OsNAC3 regulates seed germination by influencing cell elongation of the embryo through directly affecting OsEXP4 expression and indirectly ABA-medicated OsEXP4 expression. The OsNAC3 elite haplotype is useful for genetic improvement of seed germination, and overexpression of OsNAC3 can significantly increase seed germination. We therefore propose that OsNAC3 is a potential target in breeding of rice varieties with high seed germination for direct seeding cultivation.

Genome-wide identification of PYL/PYR-PP2C (A)-SnRK2 genes in Eutrema and their co-expression analysis in response to ABA and abiotic stresses

ABA signaling core components PYR/PYL, group A PP2C and SnRK2 play important roles in various environmental stress responses of plants. This study identified 14 PYR/PYL, 9 PP2C (A), and 10 SnRK2 genes from halophytic Eutrema. Phylogenetic analysis showed 4 EsPYR/PYL, 4 EsPP2C (A) and 3 EsSnRK2 subfamilies characterized, which was supported by their gene structures and protein motifs. Large-scale segmental duplication event was demonstrated to be a major contributor to expansion of the EsPYL-PP2C (A)-SnRK2 gene families. Synteny relationship analysis revealed more orthologous PYL-PP2C (A)-SnRK2 gene pairs located in collinear blocks between Eutrema and Brassica than that between Eutrema and Arabidopsis. RNA-seq and qRT-PCR revealed EsABI1, EsABI2 and EsHAL2 showed a significantly up-regulated expression in leaves and roots in response to ABA, NaCl or cold stress. Three markedly co-expression modules of ABA/R-brown, NaCl/L-lightsteelblue1 and Cold/R-lightgreen were uncovered to contain EsPYL-PP2C (A)-SnRK2 genes by WGCNA analysis. GO and KEGG analysis indicated that the genes of ABA/R-brown module containing EsHAB1, EsHAI2 and EsSnRK2.6 were enriched in proteasome pathway. Further, EsHAI2-OE transgenic Arabidopsis lines showed significantly enhanced seeds germination and seedlings growth. This work provides a new insight for elucidating potential molecular functions of PYL-PP2C (A)-SnRK2 responding to ABA and abiotic stresses.

Genome-Wide Identification, Evolution and Expression Profile Analysis of NAC Transcription Factor in Simmondsia chinensis

NAC transcription factors (TFs) are one of the largest plant-specific gene families and play important roles in plant growth, development, and the biotic and abiotic stress response. Although the sequencing of Jojoba (Simmondsia chinensis) has been completed, the genome-wide identification and analysis of its NAC TFs has not been reported. In this study, a total of 57 genes were identified in Jojoba, which were divided into eight groups based on phylogenetic analysis. The genes clustered in the same groups have a similar gene structure and motif distribution. Based on the analysis of cis-elements in NAC TFs, nine cis-acting elements were identified in the promoter region that involved in light response, hormonal response, and stress response. Synteny analysis showed a greater collinearity between Jojoba and V. vinifera than Arabidopsis thaliana. The 24 genes in the Jojoba NAC TFs are derived from fragment replication, which may be the main source of NAC amplification. Gene expression analysis identified seven genes that were highly expressed in seeds. The differential expression analysis of NAC TFs in cotyledon and embryonic axis tissues showed that the expression of 10 genes was up-regulated and 1 gene was down-regulated. This study provides more information on the classification, gene structure, conserved motif, and evolution of NAC TFs in Jojoba, facilitating further exploration of their specific functional analysis in Jojoba seed development.

Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination

Seed germination is a complex, multistage developmental process that is an important step in plant development. In this study, RNA-Seq was conducted in the embryo and endosperm of unshelled germinating rice seeds. A total of 14,391 differentially expressed genes (DEGs) were identified between the dry seeds and the germinating seeds. Of these DEGs, 7109 were identified in both the embryo and endosperm, 3953 were embryo specific, and 3329 were endosperm specific. The embryo-specific DEGs were enriched in the plant-hormone signal-transduction pathway, while the endosperm-specific DEGs were enriched in phenylalanine, tyrosine, and tryptophan biosynthesis. We categorized these DEGs into early-, intermediate-, and late-stage genes, as well as consistently responsive genes, which can be enriched in various pathways related to seed germination. Transcription-factor (TF) analysis showed that 643 TFs from 48 families were differentially expressed during seed germination. Moreover, 12 unfolded protein response (UPR) pathway genes were induced by seed germination, and the knockout of OsBiP2 resulted in reduced germination rates compared to the wild type. This study enhances our understanding of gene responses in the embryo and endosperm during seed germination and provides insight into the effects of UPR on seed germination in rice.

Identification of the passion fruit (Passiflora edulis Sims) MYB family in fruit development and abiotic stress, and functional analysis of PeMYB87 in abiotic stresses

Environmental stresses are ubiquitous in agricultural cultivation, and they affect the healthy growth and development of edible tissues in passion fruit. The study of resistance mechanisms is important in understanding the adaptation and resistance of plants to environmental stresses. In this work, two differently resistant passion fruit varieties were selected, using the expression characteristics of the transcription factor MYB, to explore the resistance mechanism of the MYB gene under various environmental stresses. A total of 174 MYB family members were identified using high-quality passion fruit genomes: 98 2R-MYB, 5 3R-MYB, and 71 1R-MYB (MYB-relate). Their family information was systematically analyzed, including subcellular localization, physicochemical properties, phylogeny at the genomic level, promoter function, encoded proteins, and reciprocal regulation. In this study, bioinformatics and transcriptome sequencing were used to identify members of the PeMYB genes in passion fruit whole-genome data, and biological techniques, such as qPCR, gene clone, and transient transformation of yeast, were used to determine the function of the passion fruit MYB genes in abiotic stress tolerance. Transcriptomic data were obtained for differential expression characteristics of two resistant and susceptible varieties, three expression patterns during pulp development, and four induced expression patterns under abiotic stress conditions. We further focused on the resistance mechanism of PeMYB87 in environmental stress, and we selected 10 representative PeMYB genes for quantitative expression verification. Most of the genes were differentially induced by four abiotic stresses, among which PeMYB87 responded significantly to high-temperature-induced expression and overexpression of the PeMYB87 gene in the yeast system. The transgenic PeMYB87 in yeast showed different degrees of stress resistance under exposure to cold, high temperatures, drought, and salt stresses. These findings lay the foundation for further analysis of the biological functions of PeMYBs involved in stress resistance in passion fruit.

Upstream open reading frame-mediated upregulation of ANAC082 expression in response to nucleolar stress in Arabidopsis

Perturbations in ribosome biogenesis cause a type of cellular stress called nucleolar or ribosomal stress, which triggers adaptive responses in both animal and plant cells. The Arabidopsis ANAC082 transcription factor has been identified as a key mediator of the plant nucleolar stress response. The 5'-untranslated region (5'-UTR) of ANAC082 mRNA contains an upstream ORF (uORF) encoding an evolutionarily conserved amino acid sequence. Here, we report that this uORF mediates the upregulation of ANAC082 expression in response to nucleolar stress. When transgenic Arabidopsis plants containing a luciferase reporter gene under the control of the ANAC082 promoter and 5'-UTR were treated with reagents that induced nucleolar stress, expression of the reporter gene was enhanced in a uORF sequence-dependent manner. Additionally, we examined the effect of an endoplasmic reticulum (ER) stress-inducing reagent on reporter gene expression because the closest homolog of ANAC082 in Arabidopsis, ANAC103, is involved in the ER stress response. However, the ANAC082 uORF did not respond to ER stress. Interestingly, although ANAC103 has a uORF with an amino acid sequence similar to that of the ANAC082 uORF, the C-terminal sequence critical for regulation is not well conserved among ANAC103 homologs in Brassicaceae. Transient expression assays revealed that unlike the ANAC082 uORF, the ANAC103 uORF does not exert a sequence-dependent repressive effect. Altogether, our findings suggest that the ANAC082 uORF is important for the nucleolar stress response but not for the ER stress response, and that for this reason, the uORF sequence-dependent regulation was lost in ANAC103 during evolution.

The exodomain of the impaired oomycete susceptibility 1 receptor mediates both endoplasmic reticulum stress responses and abscisic acid signalling during downy mildew infection of Arabidopsis

The phytohormone abscisic acid (ABA) regulates cell growth and plant development, and contributes to defence responses to pathogens. We previously showed that the Arabidopsis malectin-like domain leucine-rich repeat receptor-like kinase (MLD-LRR-RLK) impaired oomycete susceptibility 1 (IOS1) attenuates ABA signalling during infection with the oomycete downy mildew pathogen Hyaloperonospora arabidopsidis. The exodomain of IOS1 with its MLD retains the receptor in the endoplasmic reticulum (ER), where it interacts with the ribophorin HAP6 to dampen a pathogen-induced ER stress response called the unfolded protein response (UPR). The down-regulation of both ABA and UPR signalling probably provides the pathogen with an advantage for infection. Here, we show that ABA-related phenotypes of the ios1-1 mutant, such as up-regulated expression of ABA-responsive genes and hypersensitivity to exogenous ABA application, were reverted by expression of the IOS1 exodomain in the mutant background. Furthermore, knockdown mutants for ER-resident HAP6 showed similarly reduced UPR and ABA signalling, indicating that HAP6 positively regulates both pathways. Our data suggest that the IOS1 exodomain and HAP6 contribute in the ER to the IOS1-mediated interference with ABA and UPR signalling.

Molecular Characterization and Drought Resistance of GmNAC3 Transcription Factor in Glycine max (L.) Merr

Soybean transcription factor GmNAC plays important roles in plant resistance to environmental stresses. In this study, GmNAC3 was cloned in the drought tolerant soybean variety “Jiyu47”, with the molecular properties of GmNAC3 characterized to establish its candidacy as a NAC transcription factor. The yeast self-activation experiments revealed the transcriptional activation activity of GmNAC3, which was localized in the nucleus by the subcellular localization analysis. The highest expression of GmNAC3 was detected in roots in the podding stage of soybean, and in roots of soybean seedlings treated with 20% PEG6000 for 12 h, which was 16 times higher compared with the control. In the transgenic soybean hairy roots obtained by the Agrobacterium-mediated method treated with 20% PEG6000 for 12 h, the activities of superoxide dismutase, peroxidase, and catalase and the content of proline were increased, the malondialdehyde content was decreased, and the expressions of stress resistance-related genes (i.e., APX2, LEA14, 6PGDH, and P5CS) were up-regulated. These expression patterns were confirmed by transgenic Arabidopsis thaliana with the overexpression of GmNAC3. This study provided strong scientific evidence to support further investigation of the regulatory function of GmNAC3 in plant drought resistance and the molecular mechanisms regulating the plant response to environmental stresses.

In-Depth Proteomic Analysis of the Secondary Dormancy Induction by Hypoxia or High Temperature in Barley Grains

In barley, incubation of primary dormant (D1) grains on water under conditions that do not allow germination, i.e. 30°C in air and 15°C or 30°C in 5% O2, induces a secondary dormancy (D2) expressed as a loss of the ability to germinate at 15°C in air. The aim of this study was to compare the proteome of barley embryos isolated from D1 grains and D2 ones after induction of D2 at 30°C or in hypoxia at 15°C or 30°C. Total soluble proteins were analyzed by 2DE gel-based proteomics, allowing the selection of 130 differentially accumulated proteins (DAPs) among 1,575 detected spots. According to the protein abundance profiles, the DAPs were grouped into six abundance-based similarity clusters. Induction of D2 is mainly characterized by a down-accumulation of proteins belonging to cluster 3 (storage proteins, proteases, alpha-amylase inhibitors and histone deacetylase HD2) and an up-accumulation of proteins belonging to cluster 4 (1-Cys peroxiredoxin, lipoxygenase2 and caleosin). The correlation-based network analysis for each cluster highlighted central protein hub. In addition, most of genes encoding DAPs display high co-expression degree with 19 transcription factors. Finally, this work points out that similar molecular events accompany the modulation of dormancy cycling by both temperature and oxygen, including post-translational, transcriptional and epigenetic regulation.

Updated role of ABA in seed maturation, dormancy, and germination

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Functional ABA biosynthesis genes show specific roles for ABA accumulation at different stages of seed development and seedling establishment.

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De novo ABA biosynthesis during embryogenesis is required for late seed development, maturation, and induction of primary dormancy.

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ABA plays multiple roles with the key LAFL hub to regulate various downstream signaling genes in seed and seedling development.

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Key ABA signaling genes ABI3, ABI4, and ABI5 play important multiple functions with various cofactors during seed development such as de-greening, desiccation tolerance, maturation, dormancy, and seed vigor.

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The crosstalk between ABA and other phytohormones are complicated and important for seed development and seedling establishment.

Background

Seed is vital for plant survival and dispersion, however, its development and germination are influenced by various internal and external factors. Abscisic acid (ABA) is one of the most important phytohormones that influence seed development and germination. Until now, impressive progresses in ABA metabolism and signaling pathways during seed development and germination have been achieved. At the molecular level, ABA biosynthesis, degradation, and signaling genes were identified to play important roles in seed development and germination. Additionally, the crosstalk between ABA and other hormones such as gibberellins (GA), ethylene (ET), Brassinolide (BR), and auxin also play critical roles. Although these studies explored some actions and mechanisms by which ABA-related factors regulate seed morphogenesis, dormancy, and germination, the complete network of ABA in seed traits is still unclear.

Aim of review

Presently, seed faces challenges in survival and viability. Due to the vital positive roles in dormancy induction and maintenance, as well as a vibrant negative role in the seed germination of ABA, there is a need to understand the mechanisms of various ABA regulators that are involved in seed dormancy and germination with the updated knowledge and draw a better network for the underlying mechanisms of the ABA, which would advance the understanding and artificial modification of the seed vigor and longevity regulation.

Key scientific concept of review

Here, we review functions and mechanisms of ABA in different seed development stages and seed germination, discuss the current progresses especially on the crosstalk between ABA and other hormones and signaling molecules, address novel points and key challenges (e.g., exploring more regulators, more cofactors involved in the crosstalk between ABA and other phytohormones, and visualization of active ABA in the plant), and outline future perspectives for ABA regulating seed associated traits.

An R2R3-MYB Transcription Factor RmMYB108 Responds to Chilling Stress of Rosa multiflora and Conferred Cold Tolerance of Arabidopsis

A sudden cooling in the early spring or late autumn negatively impacts the plant growth and development. Although a number of studies have characterized the role of the transcription factors (TFs) of plant R2R3-myeloblastosis (R2R3-MYB) in response to biotic and abiotic stress, plant growth, and primary and specific metabolisms, much less is known about their role in Rosa multiflora under chilling stress. In the present study, RmMYB108, which encodes a nuclear-localized R2R3-MYB TF with a self-activation activity, was identified based on the earlier published RNA-seq data of R. multiflora plants exposed to short-term low-temperature stress and also on the results of prediction of the gene function referring Arabidopsis. The RmMYB108 gene was induced by stress due to chilling, salt, and drought and was expressed in higher levels in the roots than in the leaves. The heterologous expression of RmMYB108 in Arabidopsis thaliana significantly enhanced the tolerance of transgenic plants to freezing, water deficit, and high salinity, enabling higher survival and growth rates, earlier flowering and silique formation, and better seed quantity and quality compared with the wild-type (WT) plants. When exposed to a continuous low-temperature stress at 4°C, transgenic Arabidopsis lines-overexpressing RmMYB108 showed higher activities of superoxide dismutase and peroxidase, lower relative conductivity, and lower malondialdehyde content than the WT. Moreover, the initial fluorescence (F _o) and maximum photosynthetic efficiency of photosystem II (F _v/F _m) changed more dramatically in the WT than in transgenic plants. Furthermore, the expression levels of cold-related genes involved in the ICE1 (Inducer of CBF expression 1)-CBFs (C-repeat binding factors)-CORs (Cold regulated genes) cascade were higher in the overexpression lines than in the WT. These results suggest that RmMYB108 was positively involved in the tolerance responses when R. multiflora was exposed to challenges against cold, freeze, salt, or drought and improved the cold tolerance of transgenic Arabidopsis by reducing plant damage and promoting plant growth.