Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings

Genome-wide analysis of the bHLH gene family in Spatholobus suberectus identifies SsbHLH112 as a regulator of flavonoid biosynthesis

Spatholobus suberectus Dunn (S. suberectus), a medicinal herb from the Leguminosae family, is widely utilized in traditional medicine. The dried stem of S. suberectus demonstrates a variety of pharmacological effects, primarily attributed to its rich content of flavonoid compounds, such as catechin. The bHLH gene family serves diverse functions in plants, including regulating flavonoid biosynthesis, yet its specific function in S. suberectus remains uncertain. To address this, the sequenced genome of S. suberectus was leveraged for an extensive genome-wide analysis of the bHLH gene family. This analysis identified 156 SsbHLH genes, which were phylogenetically classified into 19 distinct subgroups. Of these, 153 genes were mapped across 9 chromosomes, while 3 remained unlocalized. Furthermore, genes within the identical subgroups displayed preserved exon-intron arrangements and motif patterns. Ka/Ks analysis further revealed that most duplicated genes have undergone purifying selection. A subset of 12 SsbHLH genes was found to be markedly associated with flavonoid content, including catechin, isoliquiritigenin, formononetin, and genistein. Among these, SsbHLH112, which strongly correlates with catechin levels, was shown to markedly elevate flavonoids and catechin accumulation when overexpressed in Nicotiana benthamiana. This overexpression also notably upregulated NbDFR and NbLAR, consistent with increased catechin production. These results elucidate the role of SsbHLH transcription factors in flavonoid biosynthesis, providing a basis for additional exploration of SsbHLH gene functions in S. suberectus.

The GmMYB1-GmbHLHA-GmCPC-like module regulates light-induced anthocyanin production in soybean sprouts

Soybean (Glycine max L.) is an important economic crop, flavonoids (such as anthocyanins) and some other nutrients of which were significantly promoted after germination. The accumulation of anthocyanin is influenced by many kinds of factors in plants, the regulatory mechanism of which is relatively complex. Here, soybean double mutant stf1/2 was utilized and found that GmSTF1/2 participated in light-mediated anthocyanin production in soybean. GmMYB1 was considered as a direct target of GmSTF1/2. Expressing GmMYB1 in soybean hair roots and tobacco significantly promoted anthocyanin content. GmMYB1 could directly bind to the promoters of GmDFR, GmANS, and GmUFGT, thereby promoting their transcriptions. In addition, GmMYB1 interacted with GmbHLHA, and their interaction could enhance the functions of GmMYB1 in positively regulating anthocyanin accumulation. R3-MYB GmCPC-like was activated by GmMYB1 when anthocyanin was abundant. Expressing GmCPC-like significantly inhibited anthocyanin contents in soybean hair roots and tobacco. GmCPC-like inhibited anthocyanin accumulation mainly through interacting with GmMYB1 and GmbHLHA, and then decreased their positive roles in anthocyanin production. Taken together, the GmMYB1-GmbHLHA-GmCPC-like module finely regulates anthocyanin production in soybean sprouts.

A novel bHLH transcription factor, FabHLH110, is involved in regulation of anthocyanin synthesis in petals of pink-flowered strawberry

The pink-flowered strawberry is a kind of perennial herb that serves as both an ornamental plant with a range of red-colored petals and a food crop, which was produced by distant hybridization of Fragaria × Potentilla. Although there have been numerous reports on anthocyanin synthesis in strawberry fruits, the mechanism by which bHLH transcription factors regulate anthocyanin synthesis in strawberry red petals remains unclear. In this study, a total of 376 FabHLHs were finally identified, which were divided into 25 subfamilies. According to transcriptome sequencing, phylogenetic tree construction, correlation analysis and real-time fluorescence quantitative analysis, the differential gene FabHLH110 was screened out to regulate the synthesis of flower petal anthocyanin of pink-flowered strawberry. Specifically, transient overexpression of FabHLH110 in petals of pink-flowered strawberry increased anthocyanin accumulation, while virus-induced FabHLH110 gene silencing had the opposite effect, indicating FabHLH110 functioned as a positive regulator of anthocyanin biosynthesis. In addition, it was found that FabHLH110 could not bind to the promoter of FaDFR, FaANS, FaUGT and FaGST, which should interact with FaMYB10, FaMYB90 and FaMYB114 to form MBW complex to promote anthocyanin accumulation in fruit and petals of pink-flowered strawberry, respectively. Our findings provide new insight into the regulatory network of anthocyanin synthesis in petal of pink-flowered strawberry and a new strategy for breeding rich anthocyanin.

Orchestrating anthocyanin biosynthesis in fruit of fruit trees: Transcriptional, post-transcriptional, and post-translational regulation

Coloration is an important appearance quality that contributes to product value. Anthocyanins, a type of flavonoid, not only impart rich plants color, but also contribute to human health because of their antioxidant properties, such as preventing cardiovascular disease and reducing obesity. This benefit mainly stems from various fruits. Accordingly, based on the consumption demand of beauty and nutrition, the creation of fruit tree products rich in anthocyanin is becoming an important breeding goal. The synthesis of anthocyanin has been investigated in various fruits, which is modulated by a variety of endogenous and exogenous factors, including transcription factors (TFs), plant hormones, and environmental factors (such as light, low temperature, drought). However, the detailed mechanisms in fruits of fruit trees have not been thoroughly elucidated. This review comprehensively examines the regulation of anthocyanin biosynthesis at the transcriptional, post-transcriptional, and post-translational levels, which is important for the application of molecular design strategies to cultivate high-quality fruits. At the transcriptional level, TFs were summarized to directly regulate anthocyanin biosynthesis genes, target non-anthocyanin biosynthesis pathway genes, interact with other proteins to mediate anthocyanin synthesis, and regulate anthocyanin synthesis by environmental factors and plant hormones. At the post-transcriptional level, non-coding RNAs (ncRNAs) were elucidated to mediate anthocyanin synthesis. At the post-translational level, a variety of post-translational modifications, including phosphorylation, ubiquitination, sumoylation, and persulfidation, have been elucidated to exhibit crucial functions in anthocyanin biosynthesis.

MdZFP7 integrates JA and GA signals via interaction with MdJAZ2 and MdRGL3a in regulating anthocyanin biosynthesis and undergoes degradation by the E3 ubiquitin ligase MdBRG3

Jasmonic acid (JA) and gibberellin (GA) coordinate many aspects of plant growth and development, including anthocyanin biosynthesis. However, the crossover points of JA and GA signals and the pathways through which they interact to regulate anthocyanin biosynthesis are poorly understood. Here, we investigated the molecular mechanism by which the zinc finger protein (ZFP) transcription factor Malus domestica ZFP7 (MdZFP7) regulates anthocyanin biosynthesis by integrating JA and GA signals at the transcriptional and post-translational levels. MdZFP7 is a positive regulator of anthocyanin biosynthesis, which fulfills its role by directly activating the expression of MdMYB1 and enhancing the transcriptional activation of MdWRKY6 on the target genes MdDFR and MdUF3GT. MdZFP7 integrates JA and GA signals by interacting with the JA repressor apple JASMONATE ZIM-DOMAIN2 (MdJAZ2) and the GA repressor apple REPRESSOR-of-ga1-3-like 3a (MdRGL3a). MdJAZ2 weakens the transcriptional activation of MdMYB1 by MdZFP7 and disrupts the MdZFP7-MdWRKY6 interaction, thereby reducing the anthocyanin biosynthesis promoted by MdZFP7. MdRGL3a contributes to the stimulation of anthocyanin biosynthesis by MdZFP7 by sequestering MdJAZ2 from the MdJAZ2-MdZFP7 complex. The E3 ubiquitin ligase apple BOI-related E3 ubiquitin-protein ligase 3 (MdBRG3), which is antagonistically regulated by JA and GA, targets the ubiquitination degradation of MdZFP7. The MdBRG3-MdZFP7 module moves the crosstalk of JA and GA signals from the realm of transcriptional regulation and into the protein post-translational modification. In conclusion, this study not only elucidates the node-role of MdZFP7 in the integration of JA and GA signals, but also describes the transcriptional and post-translational regulatory network of anthocyanin biosynthesis with MdZFP7 as the hub.

CsMYB308 as a repressive transcription factor inhibits anthocyanin biosynthesis in tea plants

Anthocyanins in tea (Camellia sinensis) leaves enhance tea quality due to their unique health benefits. MYB transcription factors are crucial in regulating anthocyanin biosynthesis in various plant species. In this research, a typical R2R3 repressive transcription factor CsMYB308 was identified which includes an EAR motif that belongs to the SG4 subfamily and was localized in the nucleus. Antisense oligonucleotide (asODN)-mediated CsMYB308 silencing revealed that the anthocyanin synthesis of structural genes was up-regulated. Furthermore, DNA affinity purification sequencing (DAP-seq) screened downstream genes regulated by CsMYB308. Dual-luciferase reporter (DLR) results showed that CsMYB308 suppressed anthocyanin biosynthesis by regulating the transcriptional activity of CsF3'5'H, CsDFR, and CsANS and electrophoretic mobility shift assay (EMSA) proved the concrete binding sites. In addition, we elucidated the molecular mechanism of Zijuan accumulating anthocyanin at an optimal concentration by shading experiment in summer. The results could provide an agronomic strategy to enhance the utilization of fresh leaves in summer. This study also presented a new insight of the regulatory pathway involved in anthocyanin biosynthesis in tea plants.

Integrative analysis of the R2R3-MYB gene family revealed that BsMYB36 and BsMYB51 significantly regulate the accumulation of flavonoids in Bletilla striata (Orchidaceae)

The R2R3-MYB transcription factors constitute a critical family involved in a variety of biological processes. They have been found to be essential participants in flavonoid biosynthesis in various plants. Bletilla striata (Thunb.) Reichb. f. is an orchid species rich in flavonoid compounds, with anti-inflammatory and antioxidant properties. In this study, we identified 94 R2R3-MYB genes, 89 of them were classified into 22 subgroups, and 92 were mapped to 16 chromosomes. The S5 and S7 subfamilies contained three and four members, respectively which might play roles in the biosynthesis of anthocyanin, proanthocyanidin, and flavonoid. Additionally, BsR2R3-MYBs exhibited tissue-specific expression. There were 36 genes, and 35 genes exhibited high expression in roots and pseudobulbs, respectively. The 25 R2R3-MYB genes from different subfamilies showed varying responses to drought, low temperature, and MeJA treatments. Furthermore, the S5 subfamily member BsMYB51 and the S7 subfamily member BsMYB36 were heterologous expressed in A.thaliana. Phenotypic observations of A.thaliana showed that BsMYB36 and BsMYB51 could compensate for the growth differences caused by the atmyb12 and atmyb123 mutations, respectively. Moreover, the overexpression of BsMYB36 increased flavonoid content, while decreasing the accumulation of anthocyanin and proanthocyanidin in A.thaliana. The overexpression of BsMYB51 promoted the accumulation of flavonoid, anthocyanin, and proanthocyanidin. Overexpression of BsMYB36 and BsMYB51 significantly upregulated relative genes in the phenylpropanoid and flavonoid biosynthesis pathways, such as PAL, CHS, F3'H, and DFR. This study provids the foundation for exploring the regulation of flavonoid content by BsMYBs in B.striata.

Gibberellin signaling regulates pectin biosynthesis in Arabidopsis

Pectin is an abundant polysaccharide with essential roles in various biological processes. Despite considerable advances in understanding the regulatory mechanisms of pectin biosynthesis, the influence of phytohormones on this process remains unclear. Here we report that gibberellins (GA) promotes pectin biosynthesis in Arabidopsis. The DELLA proteins, as GA signaling repressors, interact with TRANSPARENT TESTA GLABRA2 (TTG2) and components of the MYB-bHLH-WD40 (MBW) complex, the key regulators of pectin biosynthesis, to repress their transcriptional regulatory activities. Furthermore, the MBW proteins and TTG2 physically interact and synergistically activate the downstream target GLABRA2, whereas this interaction and collaboration are competitively attenuated by DELLAs. Genetic analyses validate that GA-mediated pectin biosynthesis relies on functional TTG2 and MBW proteins. Moreover, the pectin biosynthesis mediated by the GA-DELLA-MBW-TTG2 module contributes to GA-regulated seedling growth. Our findings reveal the significance of the GA-DELLA-MBW-TTG2 signaling cascade in the regulation of pectin biosynthesis and plant development.

DlMYB1 positively regulates anthocyanin biosynthesis and contributes to red exocarp coloration in red-skinned longan

Red-skinned longan (Dimocarpus longan Lour.) varieties exhibit striking exocarp coloration and high potential market value. In this study, we characterized anthocyanin accumulation in the red-skinned longan RP1901 using high performance liquid chromatography (HPLC). The exocarp of RP1901 accumulated 264.2 μg g-1 fresh weight (FW) of petunidin 3-O-glucoside (Pt3G) and 28.2 μg g-1 FW of cyanidin 3-O-glucoside (Cy3G), whereas the common longan cultivar ShiXia showed no detectable levels of these pigments. Preliminary RNA-seq analysis suggested upregulation of anthocyanin pathway genes and DlMYB1 gene. RT-qPCR analysis indicated that F3'H, ANS, GST4, and DlMYB1 were significantly upregulated in the exocarp of RP1901 compared to ShiXia. Bioinformatic analysis revealed that DlMYB1 is structurally conserved across species but diverges by 12 amino acids from ShiXia (same species) and 16 amino acids from LcMYB1 in Litchi chinensis (different genus), indicating significant genetic variation between red-skinned and common longan varieties. Subcellular localization of a DlMYB1-eGFP fusion protein confirmed its nuclear localization, consistent with transcription factor function. Overexpression of DlMYB1 in Arabidopsis thaliana led to upregulated expression of AtPAL1, AtDFR, AtLDOX, and AtGST genes and significant accumulation of anthocyanin in transgenic plants. These findings demonstrate that DlMYB1 acts as a positive regulator of anthocyanin biosynthesis and plays a key role in the pigmentation of red-skinned longan RP1901.

The MdHB7L-MdICE1L-MdHOS1 Module Fine-Tunes Apple Cold Response via CBF-Dependent and CBF-Independent Pathways

Cold stress is a major environmental factor limiting crop yield, quality, and geographical distribution worldwide. The homeodomain-leucine zipper (HD-Zip) transcription factor (TF) family plays a role in regulating plant abiotic stress responses, but the underlying mechanisms remain unclear. A HD-Zip TF, MdHB7L, is identified as promoting cold tolerance in apple. MdHB7L interacts with MdICE1L, enhancing its transcriptional activation of MdCBFs, and directly binds to MdCBF promoters to activate their expression. Conversely, MdICE1L inhibits the direct binding of MdHB7L on MdCBF promoters, revealing that MdHB7L acts as a cofactor rather than a TF when interacting with MdICE1L. Using ChIP-seq and RNA-seq, MdHB7L is found to directly regulate the expression of several key genes involved in ROS scavenging and biosynthesis of anthocyanins, soluble sugars, and proline, thereby enhancing apple cold tolerance. The E3 ubiquitin ligase MdHOS1 negatively regulates cold tolerance by interacting with and mediating the degradation of MdHB7L and MdICE1L, with a preference for MdICE1L over MdHB7L. This preference inhibits the MdHOS1-MdHB7L interaction and stabilizes MdHB7L, allowing it to sustain the plant's cold response as a TF after MdICE1L degradation. These findings provide new insights into the dynamic plant response to cold stress mediated by the MdHB7L-MdICE1-MdHOS1 module.

Comprehensive transcriptome and metabolome analysis deciphers the mechanism underlying rapid xylem growth in the dominant hybrid poplar QB3

MAIN CONCLUSION

Compared with its parents, the heterosis in growth of QB3 is primarily attributed to the upregulation of auxin and brassinosteroid-related genes, as well as the induced expression of numerous xylem and phloem synthesis genes, particularly the accumulation of lignin. Interestingly, QB3 significantly increased resistance to gray mold, which may be related to anthocyanin accumulation. Our findings illuminate the complex interplay of biological mechanisms that govern the regulation of wood growth and resistance. Poplar, as a fast-growing energy species widely distributed in the northern hemisphere, has important ecological and economic value. The hybridization of poplars is very common and often can bring to the progeny superior growth and resilience traits, but the molecular mechanism of heterosis remains to be studied. Through decades of crossbreeding work, a high-growth rate hybrid offspring named QinBai3 (QB3) was selected from P. alba × (P. alba × P. glandulosa), which provided an ideal model for investigating the molecular mechanism of heterosis. We found that the plant height, ground diameter, and xylem thickness of QB3 were much higher than those of I101 and 84 K. Through transcriptome and qRT-PCR analyses, we found that the expression levels of poplar regulatory genes associated with vegetative growth, brassinosteroid (BR), and auxin hormone signaling were significantly elevated in July compared to February. Meanwhile, compared to its parents, QB3 exhibited more specifically up-regulated genes in the processes of xylem and phloem synthesis, notably PalOPS and PalPRX52. However, in response to certain abiotic stresses, such as water deprivation and UV-B exposure, more down-regulated genes were identified. Metabolome analyses indicated that QB3 significantly increased the levels of lignin and anthocyanin, a result that aligns with the transcriptome data. Additionally, chemical assays confirmed the substantial accumulation of lignin and anthocyanin in QB3, suggesting that increased lignin accumulation may enhance the stem growth rate of QB3. Surprisingly, QB3 significantly increased resistance to Botrytis cinerea B05.10, which was accompanied by anthocyanin accumulation. In addition, our study offers detailed insights into the molecular mechanisms underlying rapid growth and stress resistance in hybrid poplar, thereby providing a new theoretical foundation and practical guidance for forest genetic breeding.

RsWRKY44 participated in anthocyanin biosynthesis regulation in radish through interaction with RsMYB1a

KEY MESSAGE

RsWRKY44 transcription factor, associated with anthocyanin biosynthesis in different radish cultivars, highly facilitates the activation of RsCHI and RsUFGT genes through its interaction with RsMYB1a, thereby promoting anthocyanin production. The regulation of anthocyanin biosynthesis in radish is primarily controlled by RsMYB1a and RsbHLH4, while the involvement of other factors in this process is not well understood. This study identified a WRKY transcription factor, RsWRKY44, as a key player in anthocyanin biosynthesis regulation. The expression of RsWRKY44 showed a strong correlation with anthocyanin content across different radish cultivars. RsWRKY44 was found to be expressed in the nuclei and exhibit transactivation activity. It was observed that only when RsWRKY44 was co-expressed with RsMYB1a, anthocyanin accumulation was induced in tobacco leaves, while RsWRKY44 alone did not. Additionally, RsWRKY44, along with RsMYB1a, activated the expression of tobacco endogenous anthocyanin biosynthesis regulatory genes NtAN1a and NtAN1b, as well as the structural genes NtCHS, NtCHI, NtDFR, NtF3H, NtANS, NtUFGT in transgenic tobacco. BiFC, FLC, and DLA assays confirmed the interaction between RsWRKY44 and RsMYB1a leading to the activation of radish genes RsCHI and RsUFGT, promoting anthocyanin biosynthesis. This study sheds light on a new molecular mechanism of RsWRKY44 involved in anthocyanin biosynthesis regulation in radish.

Resequencing and Functional Analysis Revealed That BsDFR4 Could Cause the Formation of Different Flower Colors in Bletilla striata (Orchidaceae)

The formation of flower color is closely related to anthocyanin synthesis. In this study, flowers of Bletilla striata (Orchidaceae) exhibiting distinct color morphs were collected and analyzed. The HPLC results showed significantly higher total flavonoid and anthocyanin contents in purple flowers compared to pink counterparts, with increases of 2.20-fold (p < 0.01) and 15.22-fold (p < 0.01), respectively. Cyanidin was the predominant anthocyanin in B. striata. Resequencing analyses highlighted SNP as the primary variation associated with color divergence. A comprehensive screen identified 61 genes encoding enzymes critical to the flavonoid and anthocyanin biosynthesis pathways in B. striata. Among these, 16 flower-specific genes exhibited high expression levels and harbored SNP variations. Notably, a premature stop codon was identified in a gene encoding dihydroflavonol 4-reductase (DFR), leading to truncated protein synthesis and potential disruption of anthocyanin production. Further, the heterologous overexpression of BsDFR4 in Phalaenopsis aphrodite changed petal color from white to yellow-green, demonstrating that it indeed played a regulatory role in the formation of flower color. Furthermore, yeast one-hybrid assays confirmed that transcription factors BsMYB36 and BsMYB51 could directly bind to the BsDFR4 promoter, suggesting their synergistic regulation of anthocyanin biosynthesis. These results provided a conceptual basis for insights into the formation of different flower colors in Orchidaceae.

Integrated Transcriptomics and Metabolomics Reveal Key Genes and Metabolic Pathway in Flower and Fruit Color Formation of Cerasus humilis (Bge.) Sok

Anthocyanins play a pivotal role in determining the color diversity in the flowers and fruits of Cerasus humilis (Bge.) Sok. This study performed a metabolomic analysis of the flowers and fruits of two varieties differing in pigmentation phenotypes ('Jinou 1' and 'Nongda 5'), and the results indicated that the cyanidin, pelargonidin, paeonidin, and delphinidin were the main substances serving as the primary pigments contributing to their striking chromatic divergence between two varieties. Transcriptome profiling revealed that several key structural genes (ChCHS1, ChDFR, ChF3H, and ChF3'H) in the anthocyanin biosynthesis pathway exhibited significantly elevated expression levels in 'Jinou 1' compared to 'Nongda 5'. Further metabolomic and transcriptomic correlation analyses identified that ChMYB9 and ChMYB12 exhibited strong positive associations with anthocyanin pathway metabolites in both floral and fruit tissues. Notably, ChMYB9 displayed the strongest correlation with the metabolite profiles, suggesting it may serve as a core regulatory component of the anthocyanin biosynthesis. This research provides new insights into the regulatory mechanisms of anthocyanin biosynthesis in C. humilis.

Integrated transcriptome and metabolome analysis provides insights into anthocyanin biosynthesis in Cichorium intybus L

BACKGROUND

Chicory is a unique and nutritious vegetable crop. However, the molecular mechanisms underlying anthocyanin biosynthesis in chicory remain poorly understood. We combined transcriptomics and metabolomics analyses to explore the molecular basis of anthocyanin biosynthesis in red-budded (Z1) and yellow-budded (Z7) chicory.

RESULTS

Integrated transcriptomics and metabolomics analyses were performed to investigate the molecular basis of anthocyanin biosynthesis in chicory. A total of 26 key structural genes, including F3'H, DFR, CHS, and ANS, were identified and enriched in pathways such as flavonoid and anthocyanin biosynthesis. Additionally, 29 transcription factors were identified, including 11 MYB, five bHLH, and two WD40 transcription factors, with seven MYB genes upregulated and four genes downregulated, indicating their roles in regulating anthocyanin biosynthesis. Notably, the MYB transcription factor, CI35997, which is homologous to RLL2A in lettuce, was predicted to positively regulate anthocyanin biosynthesis. Other transcription factors, such as AP2/ERF, bZIP, NAC, and Trihelix, have also been implicated. Metabolomics analysis revealed that cyanidin derivatives were the main contributors to the red coloration of chicory buds, with cyanidin-3-O-(6-O-malonyl)-glucoside being the most abundant. Furthermore, a competitive relationship between lignin and anthocyanin biosynthesis was observed, wherein the downregulation of lignin-related genes enhanced anthocyanin accumulation.

CONCLUSIONS

This study identified key structural genes and transcription factors that offer molecular-level insights into anthocyanin biosynthesis in chicory. These findings provide valuable guidance for genetic improvement of chicory and other crops with high anthocyanin content.

Light regulates SlCOP1-mediated degradation of SlJAF13, a transcription factor essential for anthocyanin biosynthesis in Aft tomato fruit

When they are exposed to light, the fruit of tomato plants (Solanum lycopersicum) carrying the dominant gene Anthocyanin fruit (Aft) accumulate anthocyanins. As the regulatory mechanism underlying this accumulation remains unclear, the role played by light in the regulation of SlJAF13, a bHLH transcription factor responsible for anthocyanin biosynthesis in tomato fruit peel, was examined. Gene expression analysis, GUS staining, and immunoblotting assays revealed that light enhanced the stability of SlJAF13 protein at a post-transcriptional level rather than transcriptionally. Protein-protein interaction assays and in vitro ubiquitination analysis revealed that CONSTITUTIVE PHOTOMORPHOGENIC1 (SlCOP1), a RING E3 ubiquitin ligase, physically interacted with SlJAF13, resulting in the ubiquitination and subsequent degradation of SlJAF13. Additionally, reductions in the levels of both anthocyanins and SlJAF13 protein were observed in fruit from plants over-expressing SlCOP1, providing further evidence that the suppressive effect of SlCOP1 on anthocyanin accumulation facilitated SlJAF13 degradation. These findings confirm the role of light in the stabilization of SIJAF13 in tomato fruit and thus provide novel insight into anthocyanin regulation in an important horticultural crop species under light conditions.

Anthocyanins promote the abundance of endophytic lactic acid bacteria by reducing ROS in Medicago truncatula

The microbial community residing on the phyllosphere is influenced by many factors, including the host plant's genotype as well as its secondary metabolites. Anthocyanins are a group of flavonoids renowned for their antioxidative properties and are widely distributed across plant tissues. However, the potential impact of anthocyanins on plant-associated microbial communities remains unknown. In the model legume Medicago truncatula, we isolated a mutant named purple leaves (pl) that produces purple leaves at a young stage due to over-accumulated anthocyanins. Through sequencing 16S rRNA amplicons of phyllosphere microbes in the pl mutant, we show that anthocyanins significantly enhance the abundance of endophytic lactic acid bacteria within plant leaves. Further in vitro study revealed that anthocyanins derived from pl can significantly promote the growth of lactic acid bacteria under anaerobic conditions. The accumulated anthocyanins in pl leaves reduced reactive oxygen species (ROS), thereby creating a favorable environment for the growth of facultative anaerobic lactic acid bacteria and resultantly increasing the abundance of phyllosphere lactic acid bacteria. Our findings elucidate the role of anthocyanins in modulating the community structure of phyllosphere microbiota in M. truncatula and provide new insights into the relationship between plant secondary metabolites and phyllosphere microbiota.

GLKs directly regulate carotenoid biosynthesis via interacting with GBFs in plants

Carotenoids are vital photosynthetic pigments for plants. Golden2-like transcription factors (GLKs) are widely recognized as major regulators of Chl biosynthesis and chloroplast development. However, despite GLKs being subjected to intensive investigations, whether GLKs directly regulate carotenoid biosynthesis and the molecular mechanisms by which GLKs transcriptionally activate their target genes remain unclear. Here, we report that GLKs directly regulate carotenoid biosynthesis and activate their target genes in a G-box binding factor (GBF)-dependent manner in Arabidopsis. Both in vitro and in vivo studies reveal that GLKs physically interact with GBFs to activate transcription of phytoene synthase (PSY), the gene encoding a rate-limiting enzyme for carotenoid biosynthesis. While GLKs possess transactivation activity, they depend on GBFs to directly bind to the G-box motif to modulate PSY expression. Loss of GBFs impairs GLK function in regulating carotenoid and Chl biosynthesis. Since the G-box motif is an enriched motif in the promoters of GLK-regulated genes, the GLK-GBF regulatory module likely serves as a common mechanism underlying GLK-regulated photosynthetic pigment biosynthesis and chloroplast development. Our findings uncover a novel regulatory machinery of carotenoid biosynthesis, discover a molecular mechanism of transcriptional regulation by GLKs, and divulge GLKs as important regulators to coordinate photosynthetic pigment synthesis in plants.

Adaptive responses of plants to light stress: mechanisms of photoprotection and acclimation. A review

Plants depend on solar energy for growth via oxygenic photosynthesis. However, when light levels exceed the optimal range for photosynthesis, it causes abiotic stress and harms plant physiology. In response to excessive light, plants activate a series of signaling pathways starting from the chloroplast and affecting the entire plant, leading to stress-specific physiological changes. These signals prompt various physiological and biochemical adjustments aimed at counteracting the negative impacts of high light intensity, including photodamage and photoinhibition. Mechanisms to protect against light stress involve scavenging of chloroplastic reactive oxygen species (ROS), adjustments in chloroplast and stomatal positioning, and increased anthocyanin production to safeguard the photosynthetic machinery. Given that this machinery is a primary target for stress-induced damage, plants have evolved acclimation strategies like dissipating thermal energy via non-photochemical quenching (NPQ), repairing Photosystem II (PSII), and regulating the transcription of photosynthetic proteins. Fluctuating light presents a less severe but consistent stress, which has not been extensively studied. Nevertheless, current research indicates that state transitions and cyclic electron flow play crucial roles in helping plants adapt to varying light conditions. This review encapsulates the latest understanding of plant physiological and biochemical responses to both high light and low light stress.

Integration of transcriptomic and metabolomic analysis reveals light-regulated anthocyanin accumulation in the peel of 'Yinhongli' plum

BACKGROUND

The 'Yinhongli' cultivar of Chinese plum (Prunus salicina Lindl.) is characterized by a distinctive bicolored peel phenotype, in which anthocyanins serve as crucial determinants of both its visual characteristics and nutritional quality. However, the molecular mechanism of underlying light-dependent anthocyanin biosynthesis of plum, especially its regulatory network and pathway, need to be further studied and explored.

RESULTS

Comprehensive physiological analyses demonstrated distinct pigmentation patterns, revealing that dark-treated (YD) plum peels retained green coloration, whereas light-exposed (YL) and bag-removed samples (YDL) exhibited red pigmentation. Utilizing an integrated approach combining metabolomic and transcriptomic analyses, we identified 266 differentially accumulated flavonoids (DAFs), among which seven anthocyanin metabolites were established as principal determinants of peel coloration. Transcriptomic profiling revealed 6,900 differentially expressed genes (DEGs) between YD and YL, demonstrating significant correlations between the phenylpropanoid and flavonoid biosynthetic pathways. Through Weighted Gene Co-expression Network Analysis (WGCNA) and correlation heatmap analysis, we identified crucial regulatory networks encompassing five structural genes (PAL, 4CL, F3'H, CHI, and UFGT) and 15 candidate regulatory genes, including six light signal transduction factor genes (UVR8, COP1, PHYBs, PIF3, and HY5) and nine transcription factor genes (MYB1, MYB20, MYB73, MYB111, LHY, DRE2B, ERF5, bHLH35, and NAC87). Subsequent RT-qPCR validation demonstrated significant light-mediated up-regulation of key structural genes (PAL, F3H, CHI, 4CL, and UFGT) involved in anthocyanin biosynthesis along with positive regulatory factors (DRE2B and NAC87). Conversely, a cohort of negative regulators, including HY5, MYB1, MYB20, MYB73, MYB111, LHY, ERF5, and bHLH35, showed marked down-regulation in response to light exposure, suggesting their potential repressive roles in the light-dependent anthocyanin biosynthesis pathway.

CONCLUSIONS

This investigation provides comprehensive insights into the molecular mechanisms of anthocyanin biosynthesis in light-dependent anthocyanin biosynthesis in 'Yinhongli' plum, identifying critical structural genes and potential regulatory TFs. The findings offer substantial contributions to the understanding of anthocyanin regulation in fruit crops and provide a valuable foundation for molecular breeding initiatives aimed at enhancing quality traits in plum cultivars.

Effect of Light Intensity on Anthocyanin Synthesis Assessed Using Leaves of Aglaonema commutatum

BACKGROUND

Plant anthocyanins are a secondary metabolite widely distributed in the roots, stems, leaves, flowers, and fruits of plants, and their synthesis is significantly affected by light intensity. To investigate the synthesis of anthocyanins in Aglaonema commutatum's leaves under different light intensities is essential.

METHODS

Using the commonly colored leaf A. commutatum variety 'Emerald' as the control group, and the red-leaf varieties 'Red Ruyi', 'Angel', and 'Gilly Red' as the experimental material, three light intensities were set: 254~368 μmol·m-2·s-1 (CK), 588~678 μmol·m-2·s-1 (T1), and 1125~1267 μmol·m-2·s-1 (T2).

RESULTS

The changes in anthocyanin content and anthocyanin-related gene expression in the leaves of A. commutatum with different leaf colors under different light intensities were studied. The results show that the anthocyanin content of A. commutatum leaves had a different trend compared to A. commutatum with increasing light intensity, and the appropriate light intensity could significantly promote anthocyanin synthesis after a certain time, and vice-versa. The anthocyanin content of CK and the T1 treatment was 1.14-3.72 times that of the T2 treatment; the photosensitive genes PHYB, CRY, and UVR8 were correlated with the anthocyanin synthesis of 'Angel' and 'Gilly Red'. The anthocyanin structural genes PAL, DFR, and ANS were correlated with the anthocyanin synthesis of 'Red Ruyi', 'Angel', and 'Gilly Red'. The anthocyanin transcription factor bHLH was strongly correlated with the anthocyanin synthesis of 'Angel'.

CONCLUSIONS

As a byproduct from A. commutatum leaves with ornamental value and potential economic value, this study was helpful to understand the potential mechanism of A. commutatum's leaves where light intensity regulates anthocyanin synthesis and accumulation.

The E3 ubiquitin ligase BRG3 and the protein kinase MPK7 antagonistically regulate LBD36 turnover, a key node for integrating nitrate and gibberellin signaling in apple

Nitrate is the main source of nitrogen in plants. Nitrate stimulation causes changes in plant secondary metabolites, including anthocyanins. However, the molecular mechanism underlying how nitrate regulates anthocyanin biosynthesis remains unclear. In this study, we identified a nitrate response factor MdLBD36 in apple. This factor positively regulated nitrate deficiency-induced anthocyanin biosynthesis by promoting the transcriptional activity of MdABI5, an important regulator of anthocyanins, and directly activated MdABI5 expression. The E3 ubiquitin ligase MdBRG3 promoted the ubiquitinated degradation of MdLBD36 to reduce anthocyanin biosynthesis under nitrate-sufficient conditions. Nitrate deficiency-activated MdMPK7 maintained the stimulating effect of MdLBD36 on anthocyanin biosynthesis by counteracting the MdBRG3-mediated degradation of MdLBD36. Nitrate coordinated gibberellin (GA) signaling to regulate anthocyanin biosynthesis. The GA signaling repressor MdRGL2a contributed to MdLBD36-promoted anthocyanin biosynthesis by enhancing the MdLBD36-MdABI5 interaction and increasing the MdLBD36 transcriptional activation of MdABI5. In summary, our results elucidate the molecular framework of the coordinated regulation of the nitrate signaling response and anthocyanin biosynthesis by ubiquitination and phosphorylation. This study revealed the cross talk between nitrate and GA signaling in the regulation of anthocyanin biosynthesis and provides references for an in-depth exploration of the nitrate signal transduction pathway and its interactions with hormones.

Transcription Factor VvbHLH137 Positively Regulates Anthocyanin Accumulation in Grape (Vitis vinifera)

Grape (Vitis vinifera) is a popular fruit with a rich color, favorable taste, and high nutritional quality. The formation of the color of its berries is primarily determined by anthocyanin composition and concentration. Basic helix-loop-helix proteins (bHLHs) serve as critical modulators of anthocyanin synthesis, yet many bHLHs in grape have not been systematically studied and remain uncharacterized. In this study, we tracked and detected berry components in 'Moldova' grapes during three developmental stages using UPLC-MS/MS and identified malvidin derivatives as the primary main anthocyanins. Our transcriptome sequencing analysis revealed 40 genes and several transcription factors (TFs) involved in anthocyanin pathways and berry coloration, with VvCHS2 (Vitvi05g01044) showing the highest expression. Among TFs, six bHLH candidates were identified, and VvbHLH137 was determined to positively regulate anthocyanin synthesis. The over-expression of VvbHLH137 in Arabidopsis thaliana significantly augmented the anthocyanin content. In addition, VvbHLH137 was found to form interactions with VvMYB15, VvMYB44, and VvMYB306 to impact anthocyanin accumulation. It also directedly stimulates VvDFR and VvF3H transcription via binding to their promoters. These findings provide insights into anthocyanin synthesis in grapes and support molecular breeding efforts for grape cultivars with enhanced coloration.

CaMYBA-CaMYC-CaTTG1 complex activates the transcription of anthocyanin synthesis structural genes and regulates anthocyanin accumulation in pepper (Capsicum annuum L.) leaves

Anthocyanins are flavonoid-derived metabolites that contribute to plant and human health. At present, few studies have studied the biosynthesis and accumulation mechanism of anthocyanins in pepper leaves. The role of CaMYBA-CaMYC-CaTTG1 complex in anthocyanin biosynthesis in pepper leaves was studied. Yeast two-hybrid and dual-luciferase experiments showed that CaMYBA, CaMYC, and CaTTG1 could form an MYB-bHLH-WD40 (MBW) complex. They also have transcriptional activation on the anthocyanin synthesis structural genes CaCHS, CaCHI, CaF3H, CaF3'5'H, CaANS, CaDFR, and CaUFGT. Silencing CaMYBA or CaMYC could decrease the content of anthocyanin in pepper leaves. Transient overexpression of CaMYBA in tobacco indicated that CaMYBA determines the function of an MBW complex. Further analysis showed that CaMYBA could activate the expression of CaMYC by binding to its promoter. Overall, our study expands the understanding of the regulatory mechanism of anthocyanin synthesis in pepper leaves and has important significance for creating more pepper plants with different color patterns by gene editing engineering.

TaWRKY17 Interacts With TaWRKY44 to Promote Expression of TaDHN7 for Salt Tolerance in Wheat

Wheat is a crucial food crop, yet its production is continually threatened by abiotic stresses, particularly salt stress. Understanding the molecular mechanisms by which wheat responds to salt stress is essential for developing salt-tolerant varieties. In this study, we investigated the molecular pathway involving the wheat TaDHN7 in response to salt stress. The overexpression of TaDHN7 enhances salt tolerance and reactive oxygen species (ROS) scavenging in wheat, while the knockout of TaDHN7 significantly impairs salt tolerance. Furthermore, we identified that TaWRKY44 promotes the expression of TaDHN7 by binding to the W-box within the TaDHN7 promoter. Additionally, TaWRKY17 interacts with TaWRKY44, and this interaction enhances the protein stability of TaWRKY44 under salt stress, thereby enhancing its transcriptional regulatory capacity on TaDHN7. This study elucidates the TaWRKY17-TaWRKY44-TaDHN7 pathway in response to salt stress in wheat, providing valuable insights for the development of salt-tolerant wheat cultivars.

Warm temperature and mild drought remodel transcriptome and alter Arabidopsis responses to mite herbivory

In the context of climate change, increased temperature and decreased water availability are expected to have profound effects on plant-herbivore interactions. To gain further insight into this issue, this work focuses on the dissection of the response of the Arabidopsis thaliana plant to the mite pest Tetranychus urticae under environmental conditions that resemble climate change. Phenotypical and molecular changes were analyzed in plants grown under mild drought and/or warm temperatures. When the transcriptome results were compared in standard and altered climate conditions, a large number of genes were found to be differentially expressed. Mite infestations in these plants showed that basal alterations conditioned the subsequent response of the plant to a specific biotic stressor. Warm temperatures favored mite performance and decreased jasmonic acid accumulation. Reduced plant damage in mild drought conditions was correlated with a higher jasmonic acid accumulation and the up-regulation of many genes involved in the production of defensive compounds. In conclusion, the use of ambient conditions that resemble climate change highlighted the drastic alterations in gene expression that may occur in nature. Understanding how these changes affect specific plant-herbivore interactions is crucial to determining how global warming will affect crop production in the future.

Diverse roles of MYB transcription factors in plants

MYB transcription factors (TFs), one of the largest TF families in plants, are involved in various plant-specific processes as the central regulators, such as in phenylpropanoid metabolism, cell cycle, formation of root hair and trichome, phytohormones responses, reproductive growth and abiotic or biotic stress responses. Here we summarized multiple roles and explained the molecular mechanisms of MYB TFs in plant development and stress adaptation. The exploration of MYB TFs contributes to a better comprehension of molecular regulation in plant development and environmental adaptability.

WD40 proteins PaTTG1 interact with both bHLH and MYB to regulate trichome formation and anthocyanin biosynthesis in Platanus acerifolia

Trichome development and anthocyanin accumulation are regulated by a complex regulatory network, the MBW complexe consists of MYB, bHLH, and WD40 transcription factors. In this study, two sequences, named PaTTG1.1, and PaTTG1.2, were cloned and functionally characterized from Platanus acerifolia. Quantitative real-time PCR results showed that PaTTG1 genes were expressed in the trichomes and red leaves. Overexpression of PaTTG1.1 and PaTTG1.2 genes in Arabidopsis ttg1 mutants restored the phenotypes of ttg1 mutants that were glabrous and lacked purple anthocyanins in hypocotyls and seeds. In transgenic plants, the expression levels of the trichome regulation-related genes AtCPC, AtTRY, AtETC1, AtMYB23, and AtGL2, as well as early and late biosynthetic genes related to anthocyanin biosynthesis, were significantly upregulated. The results of the yeast two-hybrid showed that PaTTG1.1 and PaTTG1.2 proteins could physically interact with both bHLH and R2R3-MYB transcription factors from Arabidopsis and P. Acerifolia. Taken together, the results presented in this study suggest that the two PaTTG1 genes share similar functions in the regulation of trichomes and anthocyanins. However, there may be some differences in their regulatory mechanisms.

MsERF17 Promotes Ethylene-Induced Anthocyanin Biosynthesis Under Drought Conditions in Malus spectabilis Leaves

Drought is an important factor that affects plant anthocyanin biosynthesis. However, the underlying molecular mechanisms remain elusive. Ethylene response factors (ERFs) are pivotal regulators in plant growth and environmental responses, particularly in anthocyanin biosynthesis. This study investigated the leaf colour transition from green to red in Malus spectabilis under drought conditions. This transition was primarily attributed to the accumulation of anthocyanins, specifically cyanidin-3,5-diglucoside and cyanidin-3-O-galactoside. Our findings elucidate the pivotal role of MsERF17 in drought-induced anthocyanin biosynthesis. Biochemical and molecular analyses showed that MsERF17 positively regulates anthocyanin synthesis by binding to promoters of MsbHLH3 and MsF3' H, thereby activating their expression. Moreover, transient overexpression and virus-induced gene silencing of MsERF17 in fruit peel and leaves, respectively, regulated anthocyanin synthesis. The stable transformation of calli further corroborated the positive regulatory function of MsERF17 in anthocyanin biosynthesis. Our results provide novel insights into the mechanism by which MsERF17, induced by ethylene, promotes anthocyanin accumulation through the positive regulation of MsbHLH3 and MsF3'H expression under drought conditions in M. spectabilis leaves.

A Key R2R3-MYB Transcription Factor Activates Anthocyanin Biosynthesis and Leads to Leaf Reddening in Poplar Mutants

Colorful woody plants are highly valued for their ornamental qualities, and are commonly used in garden landscape design. We previously cultivated several ornamental poplar varieties from bud mutants of Populus sp. Linn. '2025' (ZL2025), each with different leaf colors. Based on transcriptome data from these varieties with varying anthocyanin pigmentation, we identified and named an R2R3-MYB gene, PdMYB113. The mRNA of PdMYB113 accumulated in the leaves of the red-leaf mutants 'QHY' and 'LHY', but barely expressed in the leaves of 'ZL2025'. The anthocyanin biosynthesis genes were upregulated, resulting in high levels of red anthocyanins (particularly Peonidin-3-O-rutinoside, Cyanidin-3-O-rutinoside, and Cyanidin-3-O-glucoside) in both OE-PdMYB113 tobacco and poplar plants. This upregulation caused a color change in the tissues from green to red or dark purple. Yeast one-hybrid and luciferase assays demonstrated that PdMYB113 activates the expression of anthocyanin biosynthesis genes, including the early anthocyanin biosynthetic gene PdCHS and the late anthocynin biosynthetic gene PdANS. Consequently, PdMYB113 is identified as a key regulator of red coloration in poplar. Additionally, PdMYB113 does not dwarf transgenic plants under normal lighting conditions. This study elucidates the regulatory mechanisms of color change in ZL2025 and highlights a crucial gene for breeding new varieties of woody plants.

Analysis of WD40 genes in kiwifruit reveals the key role of the light-induced AcTTG1-AcMYB75-AcbHLH2 complex in anthocyanin accumulation

WD40 superfamily genes are integral to various aspects of plant growth and development. Despite the economic importance and agricultural significance of the kiwifruit (Actinidia chinensis), a comprehensive characterization of the WD40 superfamily in this species remains elusive. In this study, we identified 280 WD40-encoding genes within the kiwifruit genome and systematically analyzed their phylogenetic relationships, gene structures, functional domains, and synteny. Our results reveal that AcWD40 genes exhibit diverse expression profiles with distinct spatio-temporal patterns. AcWD40.063, encoding TTG1 homolog (designated AcTTG1), was upregulated during light-induced anthocyanin accumulation. Heterologous expression, yeast two-hybrid (Y2H) interaction assays, and dual-luciferase reporter experiments revealed that AcTTG1 interacts with AcMYB75 and AcbHLH2, collectively promoting anthocyanin accumulation and enhancing the expression of anthocyanin biosynthesis genes, particularly AcANS. This study provides a robust framework for understanding the roles of AcWD40 gene family members and offers valuable insights for molecular breeding strategies aimed at improving kiwifruit quality.

The Monochoria genome provides insights into the molecular mechanisms underlying floral heteranthery

Heteranthery, the occurrence of functionally and structurally distinct stamens within a flower, represents a striking example of convergent evolution among diverse animal-pollinated lineages. Although the ecological basis of this somatic polymorphism is understood, the developmental and molecular mechanisms are largely unknown. To address this knowledge gap, we selected Monochoria elata (Pontederiaceae) as our study system due to its typical heterantherous floral structure. We constructed a chromosome-level genome assembly of M. elata, conducted transcriptomic analyses and target phytohormone metabolome analysis to explore gene networks and hormones associated with heteranthery. We focused on three key stamen characteristics-colour, spatial patterning, and filament elongation-selected for their significant roles in stamen differentiation and their relevance to the functional diversity observed in heterantherous species. Our analyses suggest that gene networks involving MelLEAFY3, MADS-box, and TCP genes regulate stamen identity, with anthocyanin influencing colour, and lignin contributing to filament elongation. Additionally, variation in jasmonic acid and abscisic acid concentration between feeding and pollinating anthers appears to contribute to their morphological divergence. Our findings highlight gene networks and hormones associated with intra-floral stamen differentiation and indicate that whole genome duplications have likely facilitated the evolution of heteranthery during divergence from other Pontederiaceae without heteranthery.

Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in petunia and identification of the putative candidate member involved in floral volatile benzenoids/phenylpropanoids metabolism

The basic helix-loop-helix (bHLH) family, a prominent group of transcription factors, is involved in plant growth, development, and secondary metabolic processes. Petunia (Petunia hybrida), a beloved and widely cultivated garden flower, boasts a diverse array of varieties, some of which exude a captivating fragrance that has garnered immense popularity. The aromatic allure of petunias primarily stems from the presence of volatile benzenoids/phenylpropanoids, the principal floral scent compounds. But whether bHLH transcription factors regulate petunia floral scent compound synthesis is not clear. In this study, we sought to screen the putative candidate member of bHLH which can be involved in the biosynthesis of benzenoids/phenylpropanoids by examining 63 members of the petunia bHLH gene family. Phylogenetic analysis of the 63 petunia bHLH proteins them into 16 subgroups. Almost all bHLH members contained alkaline/helix-loop-helix domains. Based on the reported RNA sequencing data of P. hybrida 'Mitchell', 30 assembled sequences were mapped to the bHLH genes of P. axillaris. Further qRT-PCR assays suggested that PhbHLH19 might be the putative candidate member in the biosynthesis of benzenoids/phenylpropanoids. PhbHLH19 showed higher expression levels in the petal limb but was lowly expressed at the bud stage, with a rapid increase in the expression level when flowers opened. The expression of PhbHLH19 displayed a significant positive correlation with that of PhPAL2, and the yeast one-hybrid assay verified that PhbHLH19 can bind to the promoter of PhPAL2. Moreover, a dual-luciferase assay proved the transcriptional activation of PhbHLH19 on PhPAL2. These findings suggested that PhbHLH19 might be a putative candidate in the regulation of benzenoid/phenylpropanoid synthesis by activating PhPAL2 expression.

Integrated Multiomics Analysis Sheds Light on the Mechanisms of Color and Fragrance Biosynthesis in Wintersweet Flowers

Wintersweet (Chimonanthus praecox) is known for its flowering in winter and its rich floral aroma; the whole flower is yellow and the inner petals are red. In this study, we chose the wintersweet genotypes HLT040 and HLT015 as the research materials, and studied the co-regulatory mechanism of color and fragrance of wintersweet through metabolomics and transcriptomics. This study found that there were more flavonoids in HLT015, and anthocyanins (cyanidin-3-O-rutinoside and cyanidin-3-O-glucoside) were only present in HLT015, but HLT040 contained more monoterpenes and FVBPs (phenylpropanoid volatile compounds) than HLT015. We constructed putative benzenoids and phenylpropanoid metabolism pathway as well as terpene metabolism pathways. We found some linkages between the different structural genes and metabolites for flower color and fragrance in wintersweet, and screened out 39 TFs that may be related to one or more structural genes in benzenoids and phenylpropanoid or terpene metabolism pathways. In the yeast one-hybrid assay, we found that CpERF7 was able to interact with the promoter of CpANS1, while CpbHLH50 and CpMYB21 interacted with the promoter of CpTPS4. This study provides a theoretical basis for understanding the co-regulatory mechanism of color and fragrance in wintersweet.

Molecular mapping of candidate genes in determining red color of perilla leaf

Perilla frutescens is a traditional medicinal plant and functional food in Asian communities, characterized by distinct red and green leaf types that have significant phenotypic and medicinal implications. However, the genetic mechanisms controlling anthocyanin synthesis in this species remain unclear. Genetic analysis serves as a powerful tool for investigating the pivotal genes and regulatory mechanisms governing anthocyanin accumulation in red and green perilla. In this study, an F2 segregation population was constructed from a hybrid of red and green perilla, and representative samples were subjected to mix-sequencing using BSA-seq and BSR-seq. A 6.0 Mb candidate region on chromosome 8 was identified, pinpointing PfMYB113b, PfC4H1, and PfF3H as key genes involved in anthocyanin biosynthesis. The insertion of a repeat sequence in the promoter of PfMYB113b leads to alterations in gene expression levels. Furthermore, PfMYB113b regulates the transcription of PfC4H1 and PfF3H, thereby influencing anthocyanin synthesis. These findings enhance our understanding of the genetic regulatory mechanisms underlying leaf coloration in perilla.

Functional characterization in Chimonobambusa utilis reveals the role of bHLH gene family in bamboo sheath color variation

Introduction

The basic helix-loop-helix (bHLH) proteins are a large family of transcription factors that are essential to physiology, metabolism, and development. However, the available information is limited about the bHLH gene family in Chimonobambusa utilis, which is widely cultivated in China because of its high-quality and economic value. C. utilis cultivars exhibit five natural color variations in their shoot sheaths, but the molecular mechanism behind this color diversity remains unclear.

Methods

De novo assembly was employed to obtain gene sequences. To identify pathways related to color formation, GO enrichment analysis was performed on the 44,255 functionally annotated unigenes.

Results

The transcriptomic analysis of C. utilis yielded a total of 195,977 transcripts and 75,137 unigenes after removing redundancy. The enrichment results revealed that four pathways were most strongly associated with color formation. Phylogenetic, conserved motif, and protein-protein interaction analyses, along with qRT-PCR validation, confirmed CubHLH17's role in red sheath color.

Discussion

This research not only deepens insights into the functional roles of CubHLH genes but also lays the foundation for genetic improvement of bamboo species. We suggest that these findings will contribute to both scientific research and commercial bamboo cultivation through gene editing technology in the future.

The transcription factor VvMYB44-1 plays a role in reducing grapevine anthocyanin biosynthesis at high temperature

High temperature reduces anthocyanin accumulation in various horticultural plants. However, the molecular mechanisms underlying the high-temperature-induced reduction of anthocyanin in grape (Vitis vinifera) remain poorly understood. In this study, VvMYB44-1 was identified as a transcriptional repressor of anthocyanin biosynthesis in grape berries, and its gene expression was strongly induced by high-temperature treatment. Overexpression of VvMYB44-1 inhibited anthocyanin accumulation in both grape berries and tobacco (Nicotiana tabacum) by repressing the transcription of the anthocyanin biosynthesis genes dihydroflavonol-4-reductase (VvDFR) and UDP-glucose flavonoid-3-O-glucosyltransferase (VvUFGT). Furthermore, the interaction between VvMYB44-1 and VvWDR2 competitively inhibited the formation of the MYB-bHLH-WD40 (MBW) activation complex and weakened the transcriptional activity of the complex, thereby decreasing anthocyanin accumulation. Additionally, VvMYB44-1 facilitated cytokinin (CK) accumulation by upregulating the expression of the CK synthesis gene lonely guy 8 (VvLOG8) and inhibiting the CK degradation gene CK oxidase 4(VvCKX4), thus contributing to CK-mediated anthocyanin inhibition in grape berries. Moreover, the inhibitory effect of VvMYB44-1 on anthocyanin biosynthesis and its downstream target genes was weakened with the deletion of the ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif, indicating that the EAR motif is indispensable for the inhibitory effect of VvMYB44-1 on anthocyanin biosynthesis in grapes. These results provide insights into the regulatory network of VvMYB44-1 in high-temperature-mediated anthocyanin biosynthesis in grapes.

Blue light-induced MiBBX24 and MiBBX27 simultaneously promote peel anthocyanin and flesh carotenoid biosynthesis in mango

Blue light simultaneously enhances anthocyanin and carotenoid biosynthesis in mango (Mangifera indica L.) fruit peel and flesh, respectively, but the mechanism remains unclear. In this study, two blue light-triggered zinc-finger transcription factors, MiBBX24 and MiBBX27, that positively regulate anthocyanin and carotenoid biosynthesis in mango fruit were identified. Both MiBBXs transcriptionally activate the expression of MiMYB1, a positive regulator of anthocyanin biosynthesis. Furthermore, both MiBBXs also trigger the expression of a phytoene synthase gene (MiPSY), which is essential for carotenoid biosynthesis. Ectopic expression of MiBBX24 or MiBBX27 in Arabidopsis increased anthocyanin contents, and their positive effects on anthocyanin accumulation in mango peel were confirmed through transient overexpression and virus-induced silencing. Transient expression of MiBBX24 or MiBBX27 in tomato (Solanum lycopersicum) and mango fruit flesh increased the carotenoid content, while the virus-induced silencing of MiBBX24 or MiBBX27 in the mango fruit flesh decreased carotenoid accumulation. Overall, our study results reveal that MiBBX24 and MiBBX27 simultaneously promote the biosynthesis of anthocyanin and carotenoids biosynthesis in mango fruit peel and flesh under blue light, indicating that BBX-mediated dual effects on physiological functions contribute to mango fruit pigment accumulation. Furthermore, we herein shed new light on the simultaneous transcriptional regulatory effects of a single factor on the biosynthesis of different plant pigments.

Identification of UDP-glucosyltransferase involved in the biosynthesis of phloridzin in Gossypium hirsutum

Phloridzin has various functions, including antioxidant properties and the treatment of diabetes, and has long been used in pharmaceutical and physiological research. The glycosylation of phloretin is a key step in the biosynthesis of phloridzin. In this study, a genome-wide association study (GWAS) based on phloridzin content was applied, and the key gene GhUGT88F3 for phloridzin-specific biosynthesis was identified in cotton. A single-base deletion in GhUGT88F3 in haplotype I caused a frameshift mutation, leading to premature translation termination and a significant reduction in phloridzin content. Molecular docking revealed important amino acid residues for GhUGT88F3's UDP-glucose transfer activity. Additionally, the transcription factor GhMYB330 was found to positively regulate GhUGT88F3 expression through population transcriptome analysis and LUC experiment. Moreover, phloridzin content was significantly elevated in both GhUGT88F3 and GhMYB330 overexpression transgenic plants. This study expands the diversity of UDP-glucosyltransferases in plants and offers a potential strategy for the sustainable production of bioactive compounds with therapeutic potential.

Metabolomics and Transcriptomics Jointly Explore the Mechanism of Pod Color Variation in Purple Pod Pea

Although the pod color was one of the seven characteristics Mendel studied in peas, the mechanism of color variation in peas with purple pods has not been reported. This study systemically analyzed the difference between two pea accessions with green pods (GPs) and purple pods (PPs) at two pod developmental stages from the metabolome and transcriptome levels, aiming to preliminarily explore the mechanism and of color variation in PPs and screen out the candidate genes. A total of 180 differentially accumulated metabolites (DAMs) belonged to seven flavonoid subgroups and 23 flavonoid-related differentially expressed genes (DEGs) were identified from the analysis of the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment, respectively. Among the 180 flavonoid metabolites, ten anthocyanin compounds, which were the principal pigments in PPs and might be the major reason for the purple color formation, were significantly up-accumulated in both of the different pod development stages of PPs. A transcriptome analysis revealed that eight genes encoding enzymes (C4H, CHI, F3H, F3'H, F3'5'H, DFR, ANS, and FLS) involved in the flavonoid synthesis pathway were significantly upregulated in PPs and finally resulted in the significant accumulation of flavonoid and anthocyanin metabolites. The joint analysis of two omics and a weighted gene co-expression network analysis (WGCNA) also screened out that the WD-40 protein-encoding gene, one WRKY and three MYB transcription factor genes exhibited significant upregulation in PPs, and highly correlated with several structural genes in flavonoid synthesis pathways, indicating that these genes are involved in the regulation of pod color formation in PPs. Overall, the results of this study first explored the mechanism underlying the purple color variation between PPs and GPs, and then preliminarily screened out some candidate genes responsible for the pod color formation in PPs.

The candidate gene SibHLHA regulates anthocyanin-driven purple pigmentation in Sesamum indicum flowers

Anthocyanins not only serve as critical pigments determining floral hues but also play essential roles in attracting insects for pollination, feeding animals and mitigating abiotic stress. However, the molecular mechanisms underlying the regulation of flower color in sesame has not yet been reported. In this study, an F2 population was constructed by crossing 'Ganzhi 9' (purple-flowered) with 'BS377' (white-flowered). Genetic analysis revealed that purple flower is controlled by a single locus named as SiFC (Sesamum indicum flower color). Using the BSA-seq approach, SiFC was preliminarily identified on chromosome 6, which was further mapped to a 473 kb interval using Kompetitive Allele Specific PCR (KASP) marker analysis. Moreover, functional annotation, expression profiling, and sequence analyses confirmed that the SibHLHA (Sesame10992) was the most likely candidate gene for SiFC. In addition, SibHLHA, highly homologous to AtTT8 (a key regulator in the anthocyanin synthesis pathway), was found to interact with WER-like or TTG1 proteins, enhancing anthocyanin accumulation in tobacco leaves. Furthermore, an SNP in the second exon of Sibhlha (BS377 variant) was found to alter the encoding amino acids, which affected Sibhlha binding to MYB protein and showed low anthocyanin in tobacco leaves compared with SibHLHA binding with WER-like or TTG1 proteins. These findings not only deepen our understanding of the molecular mechanisms controlling sesame corolla color, but also provide valuable insights for developing ornamental and consumable sesame varieties.

Genome-Wide Identification of the WD40 Gene Family in Walnut (Juglans regia L.) and Its Expression Profile in Different Colored Varieties

The walnut (Juglans regia) is a woody oilseed crop with high economic and food value as its kernels are edible and its hulls can be widely used in oil extraction and plugging, chemical raw materials, and water purification. Currently, red walnut varieties have emerged, attracting consumer interest due to their high nutritional values as they are rich in anthocyanins. WD40 is a widespread superfamily in eukaryotes that play roles in plant color regulation and resistance to stresses. In order to screen for JrWD40 associated with walnut color, we identified 265 JrWD40s in walnuts by genome-wide identification, which were unevenly distributed on 16 chromosomes. According to the phylogenetic tree, all JrWD40s were classified into six clades. WGD (Whole genome duplication) is the main reason for the expansion of the JrWD40 gene family. JrWD40s were relatively conserved during evolution, but their gene structures were highly varied; lower sequence similarity may be the main reason for the functional diversity of JrWD40s. Some JrWD40s were highly expressed only in red or green walnuts. In addition, we screened 16 unique JrWD40s to walnuts based on collinearity analysis. By qRT-PCR, we found that JrWD40-133, JrWD40-150, JrWD40-155, and JrWD40-206 may regulate anthocyanin synthesis through positive regulation, whereas JrWD40-65, JrWD40-172, JrWD40-191, JrWD40-224, and JrWD40-254 may inhibit anthocyanin synthesis, suggesting that these JrWD40s are key genes affecting walnut color variation.

Comprehensive genomic analysis of SmbHLH genes and the role of SmbHLH93 in eggplant anthocyanin biosynthesis

KEY MESSAGE

SmbHLH93can activate the expression of SmCHS, SmANS, SmDFR and SmF3H.Overexpression of SmbHLH93promotes anthocyanin biosynthesis. SmbHLH93can interact with SmMYB1 to promote anthocyanin accumulation. As an outstanding source of anthocyanins, eggplant (Solanum melongena L.) is extremely beneficial for human health. In the process of anthocyanin biosynthesis in eggplant, the basic helix-loop-helix (bHLH) transcription factor family plays a crucial role. However, the bHLH gene family is extensive, making it difficult to systematically screen and analyze their functions using conventional methods. We studied the phylogeny, gene structure, conserved motifs, promoter element, and chromosomal location of the 166 SmbHLH genes in the recently released eggplant genome. Through the analysis of transcriptomic data of eggplant peel treated with light, it was found that SmbHLH93 was the most responsive to light among those of unknown function. Additionally, it was discovered that SmbHLH93 plays a positive regulatory role in anthocyanin synthesis through dual-luciferase reporter assay(dual-LUC) and genetic transformation in Arabidopsis (Arabidopsis thaliana). Furthermore, experiments involving yeast two-hybrid (Y2H), luciferase complementation assay (Split-LUC), and tobacco transient transformation demonstrated that SmbHLH93 has the ability to interact with SmMYB1 in order to enhance anthocyanin accumulation. This study will serve as a foundation for exploring the role of SmbHLH transcription factors in anthocyanin biosynthesis in the future.

Regulation of Flavonoid Biosynthesis by the MYB-bHLH-WDR (MBW) Complex in Plants and Its Specific Features in Cereals

Flavonoids are a large group of secondary metabolites, which are responsible for pigmentation, signaling, protection from unfavorable environmental conditions, and other important functions, as well as providing numerous benefits for human health. Various stages of flavonoid biosynthesis are subject to complex regulation by three groups of transcription regulators-MYC-like bHLH, R2R3-MYB and WDR which form the MBW regulatory complex. We attempt to cover the main aspects of this intriguing regulatory system in plants, as well as to summarize information on their distinctive features in cereals. Published data revealed the following perspectives for further research: (1) In cereals, a large number of paralogs of MYC and MYB transcription factors are present, and their diversification has led to spatial and biochemical specialization, providing an opportunity to fine-tune the distribution and composition of flavonoid compounds; (2) Regulatory systems formed by MBW proteins in cereals possess distinctive features that are not yet fully understood and require further investigation; (3) Non-classical MB-EMSY-like complexes, WDR-independent MB complexes, and solely acting R2R3-MYB transcription factors are of particular interest for studying unique regulatory mechanisms in plants. More comprehensive understanding of flavonoid biosynthesis regulation will allow us to develop cereal varieties with the required flavonoid content and spatial distribution.

PbMYB5 transcription factor plays a role in regulating anthocyanin biosynthesis in pear (Pyrus bretschneideri Rehd) skin

The phenylacetone pathway, which encompasses flavonoids, lignin, and other compounds, is of paramount importance in determining the quality of pear fruit. Nevertheless, the precise regulatory functions of R2R3-MYB transcription factors in the metabolic pathways that regulate pear color changes remain unclear. In this study, we isolated an R2R3-PbMYB5(PbMYB5) transcription factor from 'Red Zaosu' pears and demonstrated that it influenced the expression of several genes, including PbCAD1, PbF5H, PbLAR, PbANR, and PbUFGT. The overexpression of PbMYB5 resulted in a notable elevation in anthocyanin concentration within the pear epidermis. Further research has shown that PbMYB5 is able to bind to PbANS and also has interactions with PbbHLH3 and PbbHLH33.We proposed that PbMYB5 forms a complex with PbbHLH3, PbbHLH33, and PbWD40 to activate PbANS and promote anthocyanin accumulation. This study offers new insights into the regulation of various metabolic pathways that impact fruit coloration.

Fade into you: genetic control of pigmentation patterns in red-flesh apple (Malus domestica)

The genetic basis of type 1 red-flesh color development in apple (Malus domestica) depends upon a particular allele of the MdMYB10 gene. Interestingly, type 1 red-flesh apples are fully red after fruit set, but anthocyanin pigmentation in apple fruit cortex may decrease during fruit growth and maturation, leading to variable red patterning and intensities in the mature cortical flesh. We developed a histogram-based color analysis method to quantitatively estimate pigmentation patterns. This methodology was applied to investigate the phenotypic diversity in four hybrid F1 families segregating for red-flesh color. Pigmentation patterns were found to be heritable allowing the identification of a new locus by QTL analysis. To further investigate the mechanisms involved in the spatial deposition of anthocyanin, metabolome, transcriptome and methylome comparisons between white and red flesh areas within the red-flesh genotype cv. 'R201' exhibiting flesh pigmentation patterns, was performed. Wide-targeted analysis showed that white-flesh areas accumulate more dihydrochalcones and hydroxycinnamic acids than red-flesh areas while red-flesh areas accumulate more flavonoids. Anthocyanin biosynthesis genes and anthocyanin positive regulators (MBW complex) were up-regulated in red-flesh areas, while a reduction in anthocyanin storage, transport and stability (increase of pH, down-regulation of MdGSTU22) and an increase in phenolic catabolism were concomitant with color fading process in white-flesh areas. Expression of MdGSTU22 was linked to a differentially methylated region (DMR) suggesting a potential environmental effect on the epigenetic control of gene expression involved in color fading. Altogether, these results provide the first characterization and functional identification of color fading in apple fruit flesh.

From spots to stripes: Evolution of pigmentation patterns in monkeyflowers via modulation of a reaction-diffusion system and its prepatterns

The reaction-diffusion (RD) system is widely assumed to account for many complex, self-organized pigmentation patterns in natural organisms. However, the specific configurations of such RD networks and how RD systems interact with positional information (i.e., prepatterns) that may specify the initiation conditions for the RD operation remain largely unknown. Here, we introduced a three-substance RD system underlying the formation of repetitive pigment spots and stripes in Mimulus flowers. It consists of an R2R3-MYB activator (NEGAN), an R3-MYB inhibitor (RTO), and a coactivator represented by two paralogous bHLH proteins. Through fine-scale genetic analyses, transgenic experiments, and computer simulations, we identified the causal loci contributing to the evolutionary transition from sparsely dispersed spots to longitudinal stripes. Genetic changes at these loci modulate the prepatterns of the activator and coactivator expression and the promoter activities of the inhibitor and one of the coactivator paralogs. Our findings highlight the importance of prepatterns towards a realistic description of RD systems in natural organisms, and reveal the genetic mechanism generating pattern variation through modulation of the kinetics of the RD system and its prepatterns.

MdFC2, a ferrochelatase gene, is a positive regulator of ALA-induced anthocyanin accumulation in apples

5-Aminolevulinic acid (ALA), a key biosynthetic precursor of tetrapyrrole compounds, significantly induces anthocyanin accumulation in apple (Malus × domestica Borkh.) as well as other fruits. Although the molecular mechanisms of ALA-induced anthocyanin accumulation have been reported, it remains unknown whether the metabolism of ALA is involved in ALA-induced anthocyanin accumulation. Here, we found that MdFC2, a gene encoding ferrochelatase (MdFC2), which catalyzes the generation of heme from protoporphyrin lX (PPIX), may play an important role in ALA-induced apple anthocyanin accumulation. Exogenous ALA induced the MdFC2 expression as well as anthocyanin accumulation in apple leaves, calli, and isolated fruits. MdFC2 overexpression in apple leaves or calli significantly enhanced anthocyanin accumulation as well as the expression of genes involved in anthocyanin biosynthesis, while RNA interference MdFC2 inhibited anthocyanin accumulation and the expression of genes involved in anthocyanin biosynthesis. When 2,2'-dithiodipyridine, an inhibitor of MdFC2, was added, ALA-induced anthocyanin accumulation was blocked. These results suggest that ALA-induced anthocyanin accumulation of apple may be regulated by heme or its biosynthesis, among which MdFC2 or MdFC2 may play a critical positive regulatory role. This finding provides a novel insight to explore the mechanisms of ALA-regulating physiological processes and better application of ALA in high-quality fruit production.

Multi-Omics Research Reveals the Effects of the ABA-Regulated Phenylpropanoid Biosynthesis Pathway on the UV-B Response in Rhododendron chrysanthum Pall

The growing depletion of the ozone layer has led to increased ultraviolet B (UV-B) radiation, prompting plants like the alpine Rhododendron chrysanthum Pall. (R. chrysanthum) to adapt to these harsh conditions. This study explored how abscisic acid (ABA) signaling influences R. chrysanthum's metabolic responses under UV-B stress. R. chrysanthum was treated with UV-B radiation and exogenous ABA for widely targeted metabolomics, transcriptomics, and proteomics assays, and relevant chlorophyll fluorescence parameters were also determined. It was observed that UV-B stress negatively impacts the plant's photosynthetic machinery, disrupting multiple metabolic processes. Multi-omics analysis revealed that ABA application mitigates the detrimental effects of UV-B on photosynthesis and bolsters the plant's antioxidant defenses. Additionally, both UV-B exposure and ABA treatment significantly influenced the phenylpropanoid biosynthesis pathway, activating key enzyme genes, such as 4CL, CCR, and HCT. The study also highlighted the MYB-bHLH-WD40 (MBW) complex's role in regulating this pathway and its interaction with ABA signaling components. These findings underscore ABA's crucial function in improving plant resistance to UV-B stress and offer novel insights into plant stress biology.

Integrated metabolomic and transcriptomic analysis revealed the transition of functional components in edible flower buds of Hemerocallis citrina Baroni

The edible flower buds of Hemerocallis citrina Baroni are used both as a vegetable and functional food. It has various health benefits due to the diversity of natural products. However, the establishment of functional components in the edible flower bud remains to be studied. We conducted a high-resolution metabolomic analysis of flower buds at three developmental stages, 1-2 cm, 4-6 cm, and edible (10-15 cm). Our analysis revealed 157 differential accumulated metabolites, including flavonoids (49), fatty acids (17) and terpenoids (13) while most of them decreased during flower bud development. Among them, 2 flavonoids, 2 long-chain fatty acids and 1 triterpene saponin are highly accumulated in edible flower buds. Furthermore, the expression levels of catalytic genes mirrored the changes in metabolite levels detected. These results track the dynamics of functional component accumulation during edible flower bud development, laying the theoretical basis for nutrition formation in H. citrina.