R2R3-MYB Transcription Factor NtMYB330 Regulates Proanthocyanidin Biosynthesis and Seed Germination in Tobacco (Nicotiana tabacum L.)

Mapping the molecular signature of ABA-regulated gene expression in germinating barley embryos

BACKGROUND

Abscisic acid (ABA) regulates key plant processes, including seed germination, dormancy, and abiotic stress responses. While its physiological role in germination is well-documented, the molecular mechanisms are still poorly understood. To address this, we analyzed transcriptomic and metabolomic changes in ABA-treated germinating barley (Hordeum vulgare) embryos. To map ABA-responsive gene expression across embryonic tissues, we employed the Visium Spatial Transcriptomics (10× Genomics). This approach, which remains technically challenging to be applied in plant tissues, enabled the precise localization of gene expression across six embryo regions, offering insights into tissue-specific expression patterns that cannot be resolved by traditional RNA-seq.

RESULTS

Transcriptomic analysis indicated that ABA acts primarily as a germination repressor. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses linked ABA-inhibited genes to energy metabolism, lignin biosynthesis, cell wall organization, and photosynthesis, while induced genes were associated with environmental adaptation and phytohormone signaling. Differentially expressed genes (DEGs) correlated with metabolites involved in phytohormone pathways, including gibberellins, jasmonates, brassinosteroids, salicylic acid, auxins, and ABA metabolism. Comparisons with developing seed transcriptomes suggested an ABA-associated gene expression signature in embryos. Spatial transcriptomics technique made possible the precise identification of ABA-induced transcriptional changes within distinct embryonic tissues.

CONCLUSIONS

Integrating transcriptomics, metabolomics and spatial transcriptomics defined the molecular signature of ABA-induced modulation of phytohormonal crosstalk, energy metabolism, and tissue-specific gene activity in germinating seeds. The successful use of spatial transcriptomics adds a novel layer of resolution for understanding tissue-specific ABA responses during barley seed germination. These findings offer new insights into the ABA role in seed germination and potential strategies for enhancing crop resilience.

Integrated transcriptomic and metabolomic analyses reveal regulatory networks governing hub metabolic pathways in Fraxinus hupehensis seeds during germination

Efforts to protect germplasm resources of Fraxinus hupehensis (Oleaceae)-an endangered species endemic to Dahong Mountain, Hubei Province, China-are facing difficulties due to the deep dormancy of its seeds. To elucidate the molecular regulatory networks underlying dormancy release, an integrated investigation combining physiological profiling with transcriptomic and metabolomic analyses was performed on seeds of F. hupehensis during six critical germination stages. A decrease was observed in the contents of soluble sugar, soluble starch and crude fat as the germination process progressed, with glycolysis, the tricarboxylic acid cycle and the pentose phosphate pathways providing energy. Plant hormones such as abscisic acid and gibberellin 4 exerted coordinated regulatory effects throughout this process. Differentially expressed genes and metabolites were detected in metabolic pathways including sugar metabolism, respiratory metabolism, protein synthesis and degradation, along with lipid metabolism. Notably, structural hub genes and metabolites in metabolic pathways of starch and sucrose, respiratory, phenylalanine and linoleic acid played crucial regulatory roles in seed germination. Furthermore, hub transcription factors within the APETALA2/ethylene-responsive factor, basic helix-loop-helix and MYB families were identified by weighted gene correlation network analysis. This study unveiled the regulatory mechanisms of primary metabolic hub pathways during seed germination, providing a theoretical foundation for the breeding and conserving F. hupehensis and other endangered plant species.

Gibberellin-Induced Transcription Factor SmMYB71 Negatively Regulates Salvianolic Acid Biosynthesis in Salvia miltiorrhiza

Salvia miltiorrhiza, the valuable traditional Chinese medicinal plant, has been used in clinics for thousands of years. The water-soluble salvianolic acid compounds are bioactive substances used in treating many diseases. Gibberellins (GAs) are growth-promoting phytohormones that regulate plant growth and development. Previous studies have demonstrated that GAs can promote salvianolic acid accumulation in S. miltiorrhiza; however, the underlying mechanism requires further investigation. Here, we identified a GA-induced R2R3MYB transcription factor (TF), SmMYB71, from a transcriptome library of GA-treated S. miltiorrhiza. SmMYB71 was highly expressed in the root of S. miltiorrhiza and localized to the nucleus. SmMYB71-knockout hairy roots showed higher salvianolic acid accumulation compared to wild lines. Overexpressing SmMYB71 in S. miltiorrhiza hairy roots significantly decreased the content of salvianolic acid by downregulating key salvianolic acid biosynthesis enzymes such as SmRAS and SmCYP98A14. The GCC box in the promoter of SmMYB71 can bind with SmERF115, suggesting that SmMYB71 is regulated by SmERF115 in salvianolic acid biosynthesis. These findings demonstrate a novel regulatory role of SmMYB71 in GA-mediated phenolic acid biosynthesis. With the development of CRISPR/Cas9-based genome editing technology, the SmMYB71 regulation mechanism of salvianolic acid biosynthesis provides a potential target gene for metabolic engineering to increase the quality of S. miltiorrhiza.

Proteomic analysis identified proteins that are differentially expressed in the flavonoid and carotenoid biosynthetic pathways of Camellia Nitidissima flowers

BACKGROUND

Camellia nitidissima Chi is a popular ornamental plant because of its golden flowers, which contain flavonoids and carotenoids. To understand the regulatory mechanism of golden color formation, the metabolites of C. nitidissima petals at five different developmental stages were detected, a proteome map of petals was first constructed via tandem mass tag (TMT) analysis, and the accuracy of the sequencing data was validated via parallel reaction monitoring (PRM).

RESULTS

Nineteen color components were detected, and most of these components were carotenoids that gradually accumulated, while some metabolites were flavonoids that were gradually depleted. A total of 97,647 spectra were obtained, and 6,789 quantifiable proteins were identified. Then, 1,319 differentially expressed proteins (DEPs) were found, 55 of which belong to the flavonoid and carotenoid pathways, as revealed by pairwise comparisons of protein expression levels across the five developmental stages. Notably, most DEPs involved in the synthesis of flavonoids, such as phenylalanine ammonium lyase and 4-coumarate-CoA ligase, were downregulated during petal development, whereas DEPs involved in carotenoid synthesis, such as phytoene synthase, 1-deoxy-D-xylulose-5-phosphate synthase, and β-cyclase, tended to be upregulated. Furthermore, protein‒protein interaction (PPI) network analysis revealed that these 55 DEPs formed two distinct PPI networks closely tied to the flavonoid and carotenoid synthesis pathways. Phytoene synthase and chalcone synthase exhibited extensive interactions with numerous other proteins and displayed high connectivity within the PPI networks, suggesting their pivotal biological functions in flavonoid and carotenoid biosynthesis.

CONCLUSION

Proteomic data on the flavonoid and carotenoid biosynthesis pathways were obtained, and the regulatory roles of the DEPs were analyzed, which provided a theoretical basis for further understanding the golden color formation mechanism of C. nitidissima.

Integrated metabolomic and transcriptomic analysis reveals biosynthesis mechanism of flavone and caffeoylquinic acid in chrysanthemum

BACKGROUND

Chrysanthemum morifolium 'HangBaiJu', a popular medicinal and edible plant, exerts its biological activities primarily through the presence of flavones and caffeoylquinic acids (CQAs). However, the regulatory mechanism of flavone and CQA biosynthesis in the chrysanthemum capitulum remains unclear.

RESULTS

In this study, the content of flavones and CQAs during the development of chrysanthemum capitulum was determined by HPLC, revealing an accumulation pattern with higher levels at S1 and S2 and a gradual decrease at S3 to S5. Transcriptomic analysis revealed that CmPAL1/2, CmCHS1/2, CmFNS, CmHQT, and CmHCT were key structural genes in flavones and CQAs biosynthesis. Furthermore, weighted gene co-expression correlation network analysis (WGCNA), k-means clustering, correlation analysis and protein interaction prediction were carried out in this study to identify transcription factors (TFs) associated with flavone and CQA biosynthesis, including MYB, bHLH, AP2/ERF, and MADS-box families. The TFs CmERF/PTI6 and CmCMD77 were proposed to act as upstream regulators of CmMYB3 and CmbHLH143, while CmMYB3 and CmbHLH143 might form a complex to directly regulate the structural genes CmPAL1/2, CmCHS1/2, CmFNS, CmHQT, and CmHCT, thereby controlling flavone and CQA biosynthesis.

CONCLUSIONS

Overall, these findings provide initial insights into the TF regulatory network underlying flavones and CQAs accumulation in the chrysanthemum capitulum, which laid a theoretical foundation for the quality improvement of C. morifolium 'HangBaiJu' and the high-quality development of the industry.

Transcriptomic and metabolomic profiling reveals molecular regulatory network involved in flower development and phenotypic changes in two Lonicera macranthoides varieties

Due to the medicinal importance of the flowers of Xianglei type (XL) Lonicera macranthoides, it is important to understand the molecular mechanisms that underlie their development. In this study, we elucidated the transcriptomic and metabolomic mechanisms that underlie the flower development mechanism of two L. macranthoides varieties. In this study, 3435 common differentially expressed unigenes (DEGs) and 1138 metabolites were identified. These common DEGs were mainly enriched in plant hormone signal transduction pathways. Metabolomic analysis showed that amino acids were the main metabolites of differential accumulation in wild-type (WT) L. macranthoides, whereas in XL, they were flavonoids and phenylalanine metabolites. Genes and transcription factors (TFs), such as MYB340, histone deacetylase 1 (HDT1), small auxin-up RNA 32 (SAUR32), auxin response factor 6 (ARF6), PIN-LIKES 7 (PILS7), and WRKY6, likely drive metabolite accumulation. Plant hormone signals, especially auxin signals, and various TFs induce downstream flower organ recognition genes, resulting in a differentiation of the two L. macranthoides varieties in terms of their developmental trajectories. In addition, photoperiodic, autonomous, and plant hormone pathways jointly regulated the L. macranthoides corolla opening. SAUR32, Arabidopsis response regulator 9 (ARR9), Gibberellin receptor (GID1B), and Constans-like 10 (COL10) were closely related to the unfolding of the L. macranthoides corolla. These findings offer valuable understanding of the flower growth process of L. macranthoides and the excellent XL phenotypes at the molecular level.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04019-1.

Analyzing the Diversity of MYB Family Response Strategies to Drought Stress in Different Flax Varieties Based on Transcriptome Data

The MYB transcription factor family has numerous members, and is involved in biological activities, such as ABA signaling, which plays an important role in a plant's resistance to abiotic stresses such as drought. However, the diversity of MYB members that respond to drought stress and their regulatory mechanisms in different flax varieties were unclear. In this study, we obtained 855.69 Gb of clean data from 120 flax root samples from 20 flax (Linum usitatissimum L.) varieties, assembled 92,861 transcripts, and identified 434 MYB family members in each variety. The expression profiles of the MYB transcription factor family from 20 flax varieties under drought stress were analyzed. The results indicated that there are four strategies by which the MYB family responds to drought stress in these 20 flax varieties, each of which has its own specific processes, such as development, reproduction, and localization processes. The four strategies also include common biological processes, such as stimulus responses, metabolic processes, and biological regulation. The WGCNA method was subsequently employed to identify key members of the MYB family involved in response strategies to drought stress. The results demonstrated that a 1R-MYB subfamily gene co-expression network is significantly related to the gibberellin response and cytokinin-activated signaling pathway processes in the 'Strategy 4' for MYB family response to drought, identifying core genes such as Lus.scaffold70.240. Our results showed a diversity of MYB family responses to drought stress within flax varieties, and these results contribute to deciphering the mechanisms of the MYB family regulation of drought resistance. This will promote the more accurate breeding development of flax to adapt to agricultural production under drought conditions.

FaMYB5 Interacts with FaBBX24 to Regulate Anthocyanin and Proanthocyanidin Biosynthesis in Strawberry (Fragaria × ananassa)

MYB and BBX transcription factors play important roles in flavonoid biosynthesis. Here, we obtained transgenic woodland strawberry with stable overexpression of FaMYB5, demonstrating that FaMYB5 can increase anthocyanin and proanthocyanidin content in roots, stems and leaves of woodland strawberry. In addition, bimolecular fluorescence complementation assays and yeast two-hybridization demonstrated that the N-terminal (1-99aa) of FaBBX24 interacts with FaMYB5. Transient co-expression of FaBBX24 and FaMYB5 in cultivated strawberry 'Xiaobai' showed that co-expression strongly promoted the expression of F3'H, 4CL-2, TT12, AHA10 and ANR and then increased the content of anthocyanin and proanthocyanidin in strawberry fruits. We also determined that FaBBX24 is also a positive regulator of anthocyanin and proanthocyanidin biosynthesis in strawberry. The results reveal a novel mechanism by which the FaMYB5-FaBBX24 module collaboratively regulates anthocyanin and proanthocyanidin in strawberry fruit.

Genome-Wide Identification of the WD40 Gene Family in Tomato (Solanum lycopersicum L.)

WD40 proteins are a superfamily of regulatory proteins widely found in eukaryotes that play an important role in regulating plant growth and development. However, the systematic identification and characterization of WD40 proteins in tomato (Solanum lycopersicum L.) have not been reported. In the present study, we identified 207 WD40 genes in the tomatoes genome and analyzed their chromosomal location, gene structure and evolutionary relationships. A total of 207 tomato WD40 genes were classified by structural domain and phylogenetic tree analyses into five clusters and 12 subfamilies and were found to be unevenly distributed across the 12 tomato chromosomes. We identified six tandem duplication gene pairs and 24 segmental duplication pairs in the WD40 gene family, with segmental duplication being the major mode of expansion in tomatoes. Ka/Ks analysis revealed that paralogs and orthologs of WD40 family genes underwent mainly purifying selection during the evolutionary process. RNA-seq data from different tissues and developmental periods of tomato fruit development showed tissue-specific expression of WD40 genes. In addition, we constructed four coexpression networks according to the transcriptome and metabolome data for WD40 proteins involved in fruit development that may be related to total soluble solid formation. The results provide a comprehensive overview of the tomato WD40 gene family and will provide valuable information for the validation of the function of tomato WD40 genes in fruit development.

Systematic investigation of the R2R3-MYB gene family in Aquilaria sinensis reveals a transcriptional repressor AsMYB054 involved in 2-(2-phenylethyl)chromone biosynthesis

Trees in the genus Aquilaria produce agarwood, a valuable resin used in medicine, perfumes, and incense. 2-(2-Phenethyl)chromones (PECs) are characteristic components of agarwood; however, molecular mechanisms underlying PEC biosynthesis and regulation remain largely unknown. The R2R3-MYB transcription factors play important regulatory roles in the biosynthesis of various secondary metabolites. In this study, 101 R2R3-MYB genes in Aquilaria sinensis were systematically identified and analyzed at the genome-wide level. Transcriptomic analysis revealed that 19 R2R3-MYB genes were significantly regulated by an agarwood inducer, and showed significant correlations with PEC accumulation. Expression and evolutionary analyses revealed that AsMYB054, a subgroup 4 R2R3-MYB, was negatively correlated with PEC accumulation. AsMYB054 was located in the nucleus and functioned as a transcriptional repressor. Moreover, AsMYB054 could bind to the promoters of the PEC biosynthesis related genes AsPKS02 and AsPKS09, and inhibit their transcriptional activity. These findings suggested that AsMYB054 functions as a negative regulator of PEC biosynthesis via the inhibition of AsPKS02 and AsPKS09 in A. sinensis. Our results provide a comprehensive understanding of the R2R3-MYB subfamily in A. sinensis and lay a foundation for further functional analyses of R2R3-MYB genes in PEC biosynthesis.

UV-C Promotes the Accumulation of Flavane-3-ols in Juvenile Fruit of Grape through Positive Regulating VvMYBPA1

Flavane-3-ol monomers are the precursors of proanthocyanidins (PAs), which play a crucial role in grape resistance. Previous studies showed that UV-C positively regulated leucoanthocyanidin reductase (LAR) enzyme activity to promote the accumulation of total flavane-3-ols in juvenile grape fruit, but its molecular mechanism was still unclear. In this paper, we found that the contents of flavane-3-ol monomers increased dramatically at the early development stage grape fruit after UV-C treatment, and the expression of its related transcription factor VvMYBPA1 was also enhanced significantly. The contents of (-)-epicatechin and (+)-catechin, the expression level of VvLAR1 and VvANR, and the activities of LAR and anthocyanidin reductase (ANR) were improved significantly in the VvMYBPA1 overexpressed grape leaves compared to the empty vector. Both VvMYBPA1 and VvMYC2 could interact with VvWDR1 using bimolecular fluorescence complementation (BiFC) and yeast two hybrid (Y2H). Finally, VvMYBPA1 was proven to bind with the promoters of VvLAR1 and VvANR by yeast one hybrid (Y1H). To sum up, we found that the expression of VvMYBPA1 increased in the young stage of grape fruit after UV-C treatment. VvMYBPA1 formed a trimer complex with VvMYC2 and VvWDR1 to regulate the expression of VvLAR1 and VvANR, thus positively promoting the activities of LAR and ANR enzyme, and eventually improved the accumulation of flavane-3-ols in grape fruit.

Transcriptome and proteome analyses reveal the potential mechanism of seed dormancy release in Amomum tsaoko during warm stratification

BACKGROUND

In Amomum tsaoko breeding, the low germination rate is the major limitation for their large-scale reproduction. We found that warm stratification was an effective treatment to break the seed dormancy of A. tsaoko prior to sowing and could be an important component of improving breeding programs. The mechanism of seed dormancy release during warm stratification remains unclear. Therefore, we studied the differences between transcripts and proteomes at 0, 30, 60, and 90 days of warm stratification, to identify some regulatory genes and functional proteins that may cause seed dormancy release in A. tsaoko and reveal their regulatory mechanism.

RESULTS

RNA-seq was performed for the seed dormancy release process, and the number of differentially expressed genes (DEGs) was 3196 in three dormancy release periods. Using TMT-labelling quantitative proteome analysis, a total of 1414 proteins were defined as differentially expressed proteins (DEPs). Functional enrichment analyses revealed that the DEGs and DEPs were mainly involved in signal transduction pathways (MAPK signaling, hormone) and metabolism processes (cell wall, storage and energy reserves), suggesting that these differentially expressed genes and proteins are somehow involved in response to seed dormancy release process, including MAPK, PYR/PYL, PP2C, GID1, GH3, ARF, AUX/IAA, TPS, SPS, and SS. In addition, transcription factors ARF, bHLH, bZIP, MYB, SBP, and WRKY showed differential expression during the warm stratification stage, which may relate to dormancy release. Noteworthy, XTH, EXP, HSP and ASPG proteins may be involved in a complex network to regulate cell division and differentiation, chilling response and the seed germination status in A. tsaoko seed during warm stratification.

CONCLUSION

Our transcriptomic and proteomic analysis highlighted specific genes and proteins that warrant further study in fully grasping the precise molecular mechanisms that control the seed dormancy and germination of A. tsaoko. A hypothetical model of the genetic regulatory network provides a theoretical basis for overcoming the physiological dormancy in A. tsaoko in the future.

Integrative analysis of sensory evaluation and non-targeted metabolomics to unravel tobacco leaf metabolites associated with sensory quality of heated tobacco

INTRODUCTION

Heated tobacco (Nicotiana tabacum L.) products are heating tobacco plug at a temperature of 350°C and produce different emissions in aerosol and sensory perceptions of tobacco leaf compared with combustible tobacco. Previous study assessed different tobacco varieties in heated tobacco for sensory quality and analyzed the links between sensory scores of the final products and certain chemical classes in tobacco leaf. However, contribution of individual metabolites to sensory quality of heated tobacco remains largely open for investigation.

METHODS

In present study, five tobacco varieties were evaluated as heated tobacco for sensory quality by an expert panel and the volatile and non-volatile metabolites were analyzed by non-targeted metabolomics profiling.

RESULTS

The five tobacco varieties had distinct sensory qualities and can be classified into higher and lower sensory rating classes. Principle component analysis and hierarchical cluster analysis showed that leaf volatile and non-volatile metabolome annotated were grouped and clustered by sensory ratings of heated tobacco. Orthogonal projections to latent structures discriminant analysis followed by variable importance in projection and fold-change analysis revealed 13 volatiles and 345 non-volatiles able to discriminate the tobacco varieties with higher and lower sensory ratings. Some compounds such as β-damascenone, scopoletin, chlorogenic acids, neochlorogenic acids, and flavonol glycosyl derivatives had strong contribution to the prediction of sensory quality of heated tobacco. Several lyso-phosphatidylcholine and lyso-phosphatidylethanolamine lipid species, and reducing and non-reducing sugar molecules were also positively related to sensory quality.

DISCUSSION

Taken together, these discriminating volatile and non-volatile metabolites support the role of leaf metabolites in affecting the sensory quality of heated tobacco and provide new information on the types of leaf metabolites that can be used to predict applicability of tobacco varieties for heated tobacco products.