A single amino acid mutant in the EAR motif of IbMYB44.2 reduced the inhibition of anthocyanin accumulation in the purple-fleshed sweetpotato

BnaABF3 and BnaMYB44 regulate the transcription of zeaxanthin epoxidase genes in carotenoid and abscisic acid biosynthesis

Zeaxanthin epoxidase (ZEP) is a key enzyme that catalyzes the conversion of zeaxanthin to violaxanthin in the carotenoid and abscisic acid (ABA) biosynthesis pathways. The rapeseed (Brassica napus) genome has 4 ZEP (BnaZEP) copies that are suspected to have undergone subfunctionalization, yet the 4 genes' underlying regulatory mechanisms remain unknown. Here, we genetically confirmed the functional divergence of the gene pairs BnaA09.ZEP/BnaC09.ZEP and BnaA07.ZEP/BnaC07.ZEP, which encode enzymes with tissue-specific roles in carotenoid and ABA biosynthesis in flowers and leaves, respectively. Molecular and transgenic experiments demonstrated that each BnaZEP pair is transcriptionally regulated via ABA-responsive element-binding factor 3 s (BnaABF3s) and BnaMYB44s as common and specific regulators, respectively. BnaABF3s directly bound to the promoters of all 4 BnaZEPs and activated their transcription, with overexpression of individual BnaABF3s inducing BnaZEP expression and ABA accumulation under drought stress. Conversely, loss of BnaABF3s function resulted in lower expression of several genes functioning in carotenoid and ABA metabolism and compromised drought tolerance. BnaMYB44s specifically targeted and repressed the expression of BnaA09.ZEP/BnaC09.ZEP but not BnaA07.ZEP/BnaC07.ZEP. Overexpression of BnaA07.MYB44 resulted in increased carotenoid content and an altered carotenoid profile in petals. Additionally, RNA-seq analysis indicated that BnaMYB44s functions as a repressor in phenylpropanoid and flavonoid biosynthesis. These findings provide clear evidence for the subfunctionalization of duplicated genes and contribute to our understanding of the complex regulatory network involved in carotenoid and ABA biosynthesis in B. napus.

A novel three-layer module BoMYB1R1-BoMYB4b/BoMIEL1-BoDFR1 regulates anthocyanin accumulation in kale

Anthocyanin is an important pigment responsible for plant coloration and beneficial to human health. Kale (Brassica oleracea var. acephala), a primary cool-season flowers and vegetables, is an ideal material to study anthocyanin biosynthesis and regulation mechanisms due to its anthocyanin-rich leaves. However, the underlying molecular mechanism of anthocyanin accumulation in kale remains poorly understood. Previously, we demonstrated that BoDFR1 is a key gene controlling anthocyanin biosynthesis in kale. Here, we discovered a 369-bp InDel variation in the BoDFR1 promoter between the two kale inbred lines with different pink coloration, which resulted in reduced transcriptional activity of the BoDFR1 gene in the light-pink line. With the 369-bp insertion as a bait, an R2R3-MYB repressor BoMYB4b was identified using the yeast one-hybrid screening. Knockdown of the BoMYB4b gene led to increased BoDFR1 expression and anthocyanin accumulation. An E3 ubiquitin ligase, BoMIEL1, was found to mediate the degradation of BoMYB4b, thereby promoting anthocyanin biosynthesis. Furthermore, the expression level of BoMYB4b was significantly reduced by light signals, which was attributed to the direct repression of the light-signaling factor BoMYB1R1 on the BoMYB4b promoter. Our study revealed that a novel regulatory module comprising BoMYB1R1, BoMIEL1, BoMYB4b, and BoDFR1 finely regulates anthocyanin accumulation in kale. The findings aim to establish a scientific foundation for genetic improvement of leaf color traits in kale, meanwhile, providing a reference for plant coloration studies.

Identification and expression analysis of the GLK gene family in tea plant (Camellia sinensis) and a functional study of CsGLK54 under low-temperature stress

The Golden2-like (GLK) transcription factor family is a significant group of transcription factors in plantae. The currently available studies have shown that GLK transcription factors have been studied mainly in chloroplast growth and development, with fewer studies in abiotic stress regulation. In this study, all tea plant GLK transcription factors were identified for the first time in tea plants, and genome-wide identification, phylogenetic analysis, and thematic characterization were performed to identify 66 GLK transcription factors in tea plants. These genes are categorized into seven groups, and an amino acid sequence comparison analysis is performed. This study revealed that the structure of GLK genes in tea plants is highly conserved and that these genes are distributed across 14 chromosomes. Collinearity analysis revealed 17 pairs of genes with fragment duplications and one pair of genes with tandem duplications, and the analysis of Ka/Ks ratios indicated that most of the genes underwent negative purifying selection. Analysis of promoter cis-elements revealed that the promoters of tea plant GLK genes contain a large number of cis-acting elements related to phytohormones and stress tolerance. In addition, a large number of genes contain LTR elements, suggesting that tea plant GLK genes are involved in low-temperature stress. qRT‒PCR analysis revealed that the expression of CsGLK17, CsGLK38, CsGLK54, CsGLK11 and CsGLK60 significantly increased and that the expression of CsGLK7 and CsGLK13 decreased in response to low-temperature induction. Taken together, the results of the transcription profile analysis suggested that CsGLK54 may play an important regulatory role under low-temperature stress. The subcellular localization of CsGLK54 was in the nucleus. Furthermore, CsGLK54 positively regulated the transcription levels of the NbPOD and NbSOD genes under low-temperature stress, which led to an increase in POD and SOD enzyme activities and a decrease in MDA content. These findings provide valuable insights into the regulatory mechanism of low-temperature stress in tea plants.

Comparative analysis of the MYB gene family in seven Ipomoea species

The MYB transcription factors regulate plant growth, development, and defense responses. However, information about the MYB gene family in Ipomoea species is rare. Herein, we performed a comprehensive genome-wide comparative analysis of this gene family among seven Ipomoea species, sweet potato (I. batatas), I. trifida, I. triloba, I. nil, I. purpurea, I. cairica, and I. aquatic, and identified 296, 430, 411, 291, 226, 281, and 277 MYB genes, respectively. The identified MYB genes were classified into five types: 1R-MYB (MYB-related), 2R-MYB (R2R3-MYB), 3R-MYB (R1R2R3-MYB), 4R-MYB, and 5R-MYB, and the MYB-related or R2R3-MYB type was the most abundant MYB genes in the seven species. The Ipomoea MYB genes were classed into distinct subgroups based on the phylogenetic topology and the classification of the MYB superfamily in Arabidopsis. Analysis of gene structure and protein motifs revealed that members within the same phylogenetic group presented similar exon/intron and motif organization. The identified MYB genes were unevenly mapped on the chromosomes of each Ipomoea species. Duplication analysis indicated that segmental and tandem duplications contribute to expanding the Ipomoea MYB genes. Non-synonymous substitution (Ka) to synonymous substitution (Ks) [Ka/Ks] analysis showed that the duplicated Ipomoea MYB genes are mainly under purifying selection. Numerous cis-regulatory elements related to stress responses were detected in the MYB promoters. Six sweet potato transcriptome datasets referring to abiotic and biotic stresses were analyzed, and MYB different expression genes' (DEGs') responses to stress treatments were detected. Moreover, 10 sweet potato MYB DEGs were selected for qRT-PCR analysis. The results revealed that four responded to biotic stress (stem nematodes and Ceratocystis fimbriata pathogen infection) and six responded to the biotic stress (cold, drought, and salt). The results may provide new insights into the evolution of MYB genes in the Ipomoea genome and contribute to the future molecular breeding of sweet potatoes.

Tree peony PsMYB44 negatively regulates petal blotch distribution by inhibiting dihydroflavonol-4-reductase gene expression

BACKGROUND AND AIMS

The tree peony (Paeonia suffruticosa Andr.) has been widely cultivated as a field plant, and petal blotch is one of its important traits, which not only promotes proliferation but also confers high ornamental value. However, the regulatory network controlling blotch formation remains elusive owing to the functional differences and limited conservation of transcriptional regulators in dicots.

METHODS

We performed phylogenetic analysis to identify MYB44-like transcription factors in P. suffruticosa blotched cultivar 'High noon' petals. A candidate MYB44-like transcription factor, PsMYB44, was analysed via expression pattern analysis, subcellular localization, target gene identification, gene silencing in P. suffruticosa petals and heterologous overexpression in tobacco.

KEY RESULTS

A blotch formation-related MYB44-like transcription factor, PsMYB44, was cloned. The C-terminal of the PsMYB44 amino acid sequence had a complete C2 motif that affects anthocyanin biosynthesis, and PsMYB44 was clustered in the MYB44-like transcriptional repressor branch. PsMYB44 was located in the nucleus, and its spatial and temporal expression patterns were negatively correlated with blotch formation. Furthermore, a yeast one-hybrid assay showed that PsMYB44 could target the promoter of the late anthocyanin biosynthesis-related dihydroflavonol-4-reductase (DFR) gene, and a dual-luciferase assay demonstrated that PsMYB44 could repress PsDFR promoter activity. On the one hand, overexpression of PsMYB44 significantly faded the red colour of tobacco flowers and decreased the anthocyanin content by 42.3 % by downregulating the expression level of the tobacco NtDFR gene. On the other hand, PsMYB44-silenced P. suffruticosa petals had a redder blotch colour, which was attributed to the fact that silencing PsMYB44 redirected metabolic flux to the anthocyanin biosynthesis branch, thereby promoting more anthocyanin accumulation in the petal base.

CONCLUSION

These results demonstrated that PsMYB44 negatively regulated the biosynthesis of anthocyanin by directly binding to the PsDFR promoter and subsequently inhibiting blotch formation, which helped to elucidate the molecular regulatory network of anthocyanin-mediated blotch formation in plants.

Modulation of anthocyanin accumulation in storage roots of sweetpotato by transcription factor IbMYB1-2 through direct binding to anthocyanin biosynthetic gene promoters

The storage roots of purple-fleshed sweetpotato rich in anthocyanins are considered nutrient-rich foods with health effects. However, the molecular mechanism underlying anthocyanin biosynthesis and regulation remains to be revealed. In this study, IbMYB1-2 was isolated from purple-fleshed sweetpotato "Xuzishu8". The phylogenetic and sequence analysis indicated that IbMYB1-2 belongs to the SG6 subfamily with a conserved bHLH motif. Subcellular localization analysis and transcriptional activity assay revealed that IbMYB1-2 is a key transcriptional activator and is specific to the nucleus. Agrobacterium rhizogenes-mediated overexpression of IbMYB1-2 in sweetpotato through in vivo root transgenic system led to an increase in anthocyanins in the root of sweetpotato. qRT-PCR and transcriptome analysis depicted that the transcript levels of IbMYB1-2, IbbHLH42, and eight structural genes that are associated with the synthesis of anthocyanin were upregulated in overexpressed IbMYB1-2 transgenic roots. Dual-luciferase reporter (DLR) assay and yeast one-hybrid (Y1H) assay demonstrated IbMYB1-2 binding to the promoter regions of IbbHLH42 and other anthocyanin biosynthetic genes, including IbCHS, IbCHI, IbF3H, IbDFR, IbANS, IbGSTF12, IbUGT78D2, and IbUF3GT. Moreover, IbbHLH42 was shown to be an active enhancer for the formation of MYB-bHLH-WD40 (MBW) complex, which strongly supports the promoter activities of the IbCHS, IbANS, IbUGT78D2, and IbGSTF12 genes to induce anthocyanin accumulation. Taken together, our findings not only revealed the underlying regulatory molecular mechanism of IbMYB1-2 for anthocyanin accumulation in the storage roots of sweetpotato but also uncovered a potential mechanism by which IbbHLH42 modulated anthocyanin biosynthesis through a positive feedback regulatory loop.

Lend Me Your EARs: A Systematic Review of the Broad Functions of EAR Motif-Containing Transcriptional Repressors in Plants

The ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif, defined by the consensus sequence patterns LxLxL or DLNx(x)P, is found in a diverse range of plant species. It is the most predominant form of active transcriptional repression motif identified so far in plants. Despite its small size (5 to 6 amino acids), the EAR motif is primarily involved in the negative regulation of developmental, physiological and metabolic functions in response to abiotic and biotic stresses. Through an extensive literature review, we identified 119 genes belonging to 23 different plant species that contain an EAR motif and function as negative regulators of gene expression in various biological processes, including plant growth and morphology, metabolism and homeostasis, abiotic stress response, biotic stress response, hormonal pathways and signalling, fertility, and ripening. Positive gene regulation and transcriptional activation are studied extensively, but there remains much more to be discovered about negative gene regulation and the role it plays in plant development, health, and reproduction. This review aims to fill the knowledge gap and provide insights into the role that the EAR motif plays in negative gene regulation, and provoke further research on other protein motifs specific to repressors.

Identification of Peanut AhMYB44 Transcription Factors and Their Multiple Roles in Drought Stress Responses

MYB transcription factors (TFs) comprise a large gene family that plays an important role in plant growth, development, stress responses, and defense regulation. However, their functions in peanut remain to be further elucidated. Here, we identified six AhMYB44 genes (AhMYB44-01/11, AhMYB44-05/15, and AhMYB44-06/16) in cultivated peanut. They are typical R2R3-MYB TFs and have many similarities but different expression patterns in response to drought stress, suggesting different functions under drought stress. Homologous genes with higher expression in each pair were selected for further study. All of them were nuclear proteins and had no self-transactivation activity. In addition, we compared the performances of different lines at germination, seedling, and adult stages under drought stress. After drought treatment, the overexpression of AhMYB44-11 transgenic plants resulted in the longest root length at the seedling stage. Levels of proline, soluble sugar and chlorophyll, and expression levels of stress-related genes, including P5CS1, RD29A, CBF1, and COR15A, were higher than those of the wild type (WT) at the adult stage. While the overexpression of AhMYB44-16 significantly increased the drought sensitivity of plants at all stages, with differential ABA content, the expression levels of the ABA-related genes PP2CA and ABI1 were significantly upregulated and those of ABA1 and ABA2 were significantly downregulated compared with the WT. AhMYB44-05 showed similar downregulated expression as AhMYB44-16 under drought stress, but its overexpression in Arabidopsis did not significantly affect the drought resistance of transgenic plants. Based on the results, we propose that AhMYB44-11 plays a role as a positive factor in drought tolerance by increasing the transcription abundance of stress-related genes and the accumulation of osmolytes, while AhMYB44-16 negatively regulates drought tolerance through its involvement in ABA-dependent stress response pathways.

Comparative transcriptome analysis of purple-fleshed sweet potato and its yellow-fleshed mutant provides insight into the transcription factors involved in anthocyanin biosynthesis in tuberous root

In various plant species, many transcription factors (TFs), such as MYB, bHLH, and WD40, have been identified as regulators of anthocyanin biosynthesis in underground organs. However, the regulatory elements of anthocyanin biosynthesis in the tuberous roots of sweet potato have not been elucidated yet. Here, we selected the purple-fleshed sweet potato cultivar "Zhezi1" (ZZ ^P ) and its spontaneous yellow-fleshed mutant "Xinli" (XL ^Y ) to investigate the regulatory mechanism of the anthocyanin biosynthesis in the tuberous roots of sweet potato. By analyzing the IbMYB1 genotype in ZZ ^P and XL ^Y , we found that the IbMYB1-2, a MYB TF involved in anthocyanin biosynthesis, was missing in the XL ^Y genome, which might lead to an extreme decrease in anthocyanins in XL ^Y . A comparative transcriptome analysis of ZZ ^P and XL ^Y was conducted to find the TFs involved in anthocyanin biosynthesis in ZZ ^P and XL ^Y . The anthocyanin structural genes were significantly enriched among the differentially expressed genes. Moreover, one MYB activator (IbMYB1), one bHLH (IbbHLH2), three WRKY activator candidates (IbWRKY21, IbWRKY24, and IbWRKY44), and two MYB repressors (IbMYB27 and IbMYBx-ZZ) were highly expressed in ZZ ^P accompanied with anthocyanin structural genes. We also tested the expression of these TFs in six purple- and two orange-fleshed sweet potato cultivars. Interestingly, most of these TFs were significantly positively correlated with anthocyanin contents in these cultivars. The function of the anthocyanin biosynthesis repression of IbMYB27 and IbMYBx-ZZ was verified through transient co-transformation with IbMYB1 into tobacco leaves. Further functional verification of the above TFs was conducted by Y2H, BiFC, and dual-luciferase assays. These tests showed that the MYB-bHLH-WD40/MYB-bHLH-WD40-WRKY complex activated the promoter of anthocyanin structural gene IbDFR and promoters for IbWRKY44, IbMYB27, and IbMYBx-ZZ, indicating reinforcement and feedback regulation to maintain the level of anthocyanin accumulation in the tuberous roots of purple-fleshed sweet potato. These results may provide new insights into the regulatory mechanism of anthocyanin biosynthesis and accumulation in underground organs of sweet potatoes.

VaMYB44 transcription factor from Chinese wild Vitis amurensis negatively regulates cold tolerance in transgenic Arabidopsis thaliana and V. vinifera

Heterologous expression of VaMYB44 gene in Arabidopsis and V. vinifera cv. 'Thompson Seedless' increases cold sensitivity, which is mediated by the interaction of VaMYC2 and VaTIFY5A with VaMYB44 MYB transcription factors play critical roles in plant stress response. However, the function of MYB44 under low temperature stress is largely unknown in grapes. Here, we isolated a VaMYB44 gene from Chinese wild Vitis amurensis acc. 'Shuangyou' (cold-resistant). The VaMYB44 is expressed in various organs and has lower expression levels in stems and young leaves. Exposure of the cold-sensitive V. vinifera cv. 'Thompson Seedless' and cold-resistant 'Shuangyou' grapevines to cold stress (-1 °C) resulted in differential expression of MYB44 in leaves with the former reaching 14 folds of the latter after 3 h of cold stress. Moreover, the expression of VaMYB44 was induced by exogenous ethylene, abscisic acid, and methyl jasmonate in the leaves of 'Shuangyou'. Notably, the subcellular localization assay identified VaMYB44 in the nucleus. Interestingly, heterologous expression of VaMYB44 in Arabidopsis and 'Thompson Seedless' grape increased freezing-induced damage compared to their wild-type counterparts. Accordingly, the transgenic lines had higher malondialdehyde content and electrolyte permeability, and lower activities of superoxide dismutase, peroxidase, and catalase. Moreover, the expression levels of some cold resistance-related genes decreased in transgenic lines. Protein interaction assays identified VaMYC2 and VaTIFY5A as VaMYB44 interacting proteins, and VaMYC2 could bind to the VaMYB44 promoter and promote its transcription. In conclusion, the study reveals VaMYB44 as the negative regulator of cold tolerance in transgenic Arabidopsis and transgenic grapes, and VaMYC2 and VaTIFY5A are involved in the cold sensitivity of plants by interacting with VaMYB44.