Identification of key amino acids for the evolution of promoter target specificity of anthocyanin and proanthocyanidin regulating MYB factors

Promoter replication of grape MYB transcription factor is associated with a new red flesh phenotype

KEY MESSAGE

In our study, we discovered a fragment duplication autoregulation mechanism in 'ZS-HY', which may be the reason for the phenotype of red foliage and red flesh in grapes. In grapes, MYBA1 and MYBA2 are the main genetic factors responsible for skin coloration which are located at the color loci on chromosome 2, but the exact genes responsible for color have not been identified in the flesh. We used a new teinturier grape germplasm 'ZhongShan-HongYu' (ZS-HY) which accumulate anthocyanin both in skin and flesh as experimental materials. All tissues of 'ZS-HY' contained cyanidin 3-O-(6″-p-coumaroyl glucoside), and pelargonidins were detected in skin, flesh, and tendril. Through gene expression analysis at different stage of flesh, significant differences in the expression levels of VvMYBA1 were found. Gene amplification analysis showed that the VvMYBA1 promoter is composed of two alleles, VvMYBA1a and 'VvMYBA1c-like'. An insertion of a 408 bp repetitive fragment was detected in the allele 'VvMYBA1c-like'. In this process, we found the 408 bp repetitive fragment was co-segregated with red flesh and foliage phenotype. Our results revealed that the 408 bp fragment replication insertion in promoter of 'VvMYBA1c-like' was the target of its protein, and the number of repeat fragments was related to the increase of trans-activation of VvMYBA1 protein. The activation of promoter by VvMYBA1 was enhanced by the addition of VvMYC1. In addition, VvMYBA1 interacted with VvMYC1 to promote the expression of VvGT1 and VvGST4 genes in 'ZS-HY'. The discovery of this mutation event provides new insights into the regulation of VvMYBA1 on anthocyanin accumulation in red-fleshed grape, which is of great significance for molecular breeding of red-fleshed table grapes.

Identification of a candidate gene for the I locus determining the dominant white bulb color in onion (Allium cepa L.)

KEY MESSAGE

Through a map-based cloning approach, a gene coding for an R2R3-MYB transcription factor was identified as a causal gene for the I locus controlling the dominant white bulb color in onion. White bulb colors in onion (Allium cepa L.) are determined by either the C or I loci. The causal gene for the C locus was previously isolated, but the gene responsible for the I locus has not been identified yet. To identify candidate genes for the I locus, an approximately 7-Mb genomic DNA region harboring the I locus was obtained from onion and bunching onion (A. fistulosum) whole genome sequences using two tightly linked molecular markers. Within this interval, the AcMYB1 gene, known as a positive regulator of anthocyanin production, was identified. No polymorphic sequences were found between white and red AcMYB1 alleles in the 4,860-bp full-length genomic DNA sequences. However, a 4,838-bp LTR-retrotransposon was identified in the white allele, in the 79-bp upstream coding region from the stop codon. The insertion of this LTR-retrotransposon created a premature stop codon, resulting in the replacement of 26 amino acids with seven different residues. A molecular marker was developed based on the insertion of this LTR-retrotransposon to genotype the I locus. A perfect linkage between bulb color phenotypes and marker genotypes was observed among 5,303 individuals of segregating populations. The transcription of AcMYB1 appeared to be normal in both red and white onions, but the transcription of CHS-A, which encodes chalcone synthase and is involved in the first step of the anthocyanin biosynthesis pathway, was inactivated in the white onions. Taken together, an aberrant AcMYB1 protein produced from the mutant allele might be responsible for the dominant white bulb color in onions.

Integrated metabolomics and transcriptomics reveal molecular mechanisms of corolla coloration in Rhododendron dauricum L

Rhododendron dauricum L. is a semi-evergreen shrub of high ornamental and medicinal values in Northeast China. To study the molecular mechanisms of corolla coloration in R. dauricum, integrated metabolomics and transcriptomics were performed in R. dauricum featuring purple flowers and R. dauricum var. album featuring white flowers. Comparative metabolomics revealed 25 differential metabolites in the corolla of the two distinct colors, enriched in flavonoids that are closely related to pigmentation in the flower. Differential analysis of the transcriptomics data revealed enrichment of structural genes for flavonoid biosynthesis (99 up- and 58 down-regulated, respectively, in purple corollas compared to white ones). Significantly, CHS and CHI, key genes in the early stage of anthocyanin synthesis, as well as F3H, F3'H, F3'5'H, DFR, ANS, and UFGT that promote the accumulation of pigments in the late stage of anthocyanin synthesis, were up-regulated in R. dauricum (purple color). In R. dauricum var. album, FLS were key genes determining the accumulation of flavonols. In addition, transcriptome-metabolome correlation analysis identified 16 R2R3 MYB transcription factors (out of 83 MYBs) that are important for corolla coloration. Five negative and four positive MYBs were further identified by integrated transcriptional and metabolic network analysis, revealing a key role of MYBA and MYB12 in regulating anthocyanins and flavonols, respectively. Moreover, we validated the function of RdMYBA by creating stable transgenic plants and found that RdMYBA promotes anthocyanin biosynthesis. In summary, we systematically characterized the transcriptome and metabolome of two R. dauricum cultivars with different flower colors and identified MYBs as key factors in modulating corolla coloration.

A near-complete assembly of asparagus bean provides insights into anthocyanin accumulation in pods

Asparagus bean (Vigna unguiculata ssp. sesquipedialis), a subspecies of V. unguiculata, is a vital legume crop widely cultivated in Asia for its tender pods consumed as vegetables. However, the existing asparagus bean assemblies still contain numerous gaps and unanchored sequences, which presents challenges to functional genomics research. Here, we present an improved reference genome sequence of an elite asparagus bean variety, Fengchan 6, achieved through the integration of nanopore ultra-long reads, PacBio high-fidelity reads, and Hi-C technology. The improved assembly is 521.3 Mb in length and demonstrates several enhancements, including a higher N50 length (46.4 Mb), an anchor ratio of 99.8%, and the presence of only one gap. Furthermore, we successfully assembled 14 telomeres and all 11 centromeres, including four telomere-to-telomere chromosomes. Remarkably, the centromeric regions cover a total length of 38.1 Mb, providing valuable insights into the complex architecture of centromeres. Among the 30 594 predicted protein-coding genes, we identified 2356 genes that are tandemly duplicated in segmental duplication regions. These findings have implications for defence responses and may contribute to evolutionary processes. By utilizing the reference genome, we were able to effectively identify the presence of the gene VuMYB114, which regulates the accumulation of anthocyanins, thereby controlling the purple coloration of the pods. This discovery holds significant implications for understanding the underlying mechanisms of color determination and the breeding process. Overall, the highly improved reference genome serves as crucial resource and lays a solid foundation for asparagus bean genomic studies and genetic improvement efforts.

Investigation of the role of TmMYB16/123 and their targets (TmMTP1/11) in the tolerance of Taxus media to cadmium

The toxicity and stress caused by heavy metal contamination has become an important constraint to the growth and flourishing of trees. In particular, species belonging to the genus Taxus, which are the only natural source for the anti-tumor medicine paclitaxel, are known to be highly sensitive to environmental changes. To investigate the response of Taxus spp. to heavy metal stress, we analyzed the transcriptomic profiles of Taxus media trees exposed to cadmium (Cd2+). In total, six putative genes from the metal tolerance protein (MTP) family were identified in T. media, including two Cd2+ stress inducible TMP genes (TmMTP1, TmMTP11 and Taxus media). Secondary structure analyses predicted that TmMTP1 and TmMTP11, which are members of the Zn-CDF and Mn-CDF subfamily proteins, respectively, contained six and four classic transmembrane domains, respectively. The introduction of TmMTP1/11 into the ∆ycf1 yeast cadmium-sensitive mutant strain showed that TmMTP1/11 might regulate the accumulation of Cd2+ to yeast cells. To screen the upstream regulators, partial promoter sequences of the TmMTP1/11 genes were isolated using the chromosome walking method. Several myeloblastosis (MYB) recognition elements were identified in the promoters of these genes. Furthermore, two Cd2+-induced R2R3-MYB TFs, TmMYB16 and TmMYB123, were identified. Both in vitro and in vivo assays confirmed that TmMTB16/123 play a role in Cd2+ tolerance by activating and repressing the expression of TmMTP1/11 genes. The present study elucidated new regulatory mechanisms underlying the response to Cd stress and can contribute to the breeding of Taxus species with high environmental adaptability.

BcMYB111 Responds to BcCBF2 and Induces Flavonol Biosynthesis to Enhance Tolerance under Cold Stress in Non-Heading Chinese Cabbage

Flavonols have been shown to respond to a variety of abiotic stresses in plants, including cold stress. Higher total flavonoid content was found in non-heading Chinese cabbage (NHCC, Brassica campestris (syn. Brassica rapa) ssp. chinensis) after cold stress. A non-targeted metabolome analysis showed a significant increase in flavonol content, including that of quercetin and kaempferol. Here, we found that an R2R3-MYB transcription factor, BcMYB111, may play a role in this process. BcMYB111 was up-regulated in response to cold treatment, with an accompanying accumulation of flavonols. Then, it was found that BcMYB111 could regulate the synthesis of flavonols by directly binding to the promoters of BcF3H and BcFLS1. In the transgenic hairy roots of NHCC or stable transgenic Arabidopsis, overexpression of BcMYB111 increased flavonol synthesis and accumulation, while these were reduced in virus-induced gene silencing lines in NHCC. After cold stress, the higher proline content and lower malondialdehyde (MDA) content showed that there was less damage in transgenic Arabidopsis than in the wild-type (WT). The BcMYB111 transgenic lines performed better in terms of antioxidant capacity because of their lower H₂O₂ content and higher superoxide dismutase (SOD) and peroxidase (POD) enzyme activities. In addition, a key cold signaling gene, BcCBF2, could specifically bind to the DRE element and activate the expression of BcMYB111 in vitro and in vivo. The results suggested that BcMYB111 played a positive role in enhancing the flavonol synthesis and cold tolerance of NHCC. Taken together, these findings reveal that cold stress induces the accumulation of flavonols to increase tolerance via the pathway of BcCBF2-BcMYB111-BcF3H/BcFLS1 in NHCC.

MYB Transcription Factor OsC1PLSr Involves the Regulation of Purple Leaf Sheath in Rice

Although several regulators associated with purple traits in rice have been identified, the genetic basis of the purple sheath remains unclear. In the present study, F2-1 and F2-2 populations were constructed using purple sheath (H93S) and green sheath (R1173 and YHSM), respectively. In order to identify QTL loci in purple sheaths, BSA analyses were performed on the two F2 populations. A crucial QTL for purple sheath was identified, tentatively named qPLSr6, and was located in the 4.61 Mb to 6.03 Mb region of chromosome 6. Combined with expression pattern analysis of candidate genes, LOC_Os06g10350 (OsC1PLSr) was suggested as a candidate gene. The homozygous mutant KO-1 and KO-2 created through CRISPR/Cas9 editing, lost their purple leaf sheath. The RT-PCR revealed that OsC1PLSr, anthocyanin synthase (ANS), diflavonol-4-reductase (DFR), flavanone-3-hydroxylase (F3H), and flavanone-3′-hydroxylase (F3′H) expression levels were dramatically down-regulated in the mutants. The yeast report system indicated that the 145–272 aa region at the C-terminal of OsC1PLSr is a positive transcriptional activation domain. The results indicated that OsC1PLSr synthesized anthocyanins by regulating the expression of ANS, DFR, F3H, and F3′H. This study provides new insights into the genetic basis of the purple sheath.

Novel R2R3 MYB transcription factors regulate anthocyanin synthesis in Aubergine tomato plants

BACKGROUND

A high content in anthocyanins, for their health beneficial properties, represents an added value for fruits and vegetables. Tomato (Solanum lycopersicum) is one of the most consumed vegetables worldwide and is rich in vitamins and carotenoids. In recent years, purple-skinned tomatoes, enriched of anthocyanins, were produced recovering allelic variants from wild Solanum species. The molecular basis of the Anthocyanin fruit (Aft) locus, exploited by breeders to activate the anthocyanin synthesis in tomato epicarp, has been recently identified in the correct splicing of the R2R3 MYB gene AN2like. Aubergine (Abg) is a tomato accession which introgressed from Solanum lycopersicoides a locus activating the synthesis of anthocyanins in the fruit. The Abg locus was mapped in the region of chromosome 10 containing Aft and the possibility that Abg and Aft represented alleles of the same gene was hypothesized.

RESULTS

We dissected the R2R3 MYB gene cluster located in the Abg genomic introgression and demonstrated that AN2like is correctly spliced in Abg plants and is expressed in the fruit epicarp. Moreover, its silencing specifically inhibits the anthocyanin synthesis. The Abg allele of AN2like undergoes alternative splicing and produces two proteins with different activities. Furthermore, in Abg the master regulator of the anthocyanin synthesis in tomato vegetative tissues, AN2, is very poorly expressed. Finally, a novel R2R3 MYB gene was identified: it encodes another positive regulator of the pathway, whose activity was lost in tomato and in its closest relatives.

CONCLUSION

In this study, we propose that AN2like is responsible of the anthocyanin production in Abg fruits. Unlike wild type tomato, the Abg allele of AN2like is active and able to regulate its targets. Furthermore, in Abg alternative splicing leads to two forms of AN2like with different activities, likely representing a novel type of regulation of anthocyanin synthesis in tomato.

An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit flesh color in Japanese plum

Japanese plums exhibit wide diversity of fruit coloration. The red to black hues are caused by the accumulation of anthocyanins, while their absence results in yellow, orange or green fruits. In Prunus, MYB10 genes are determinants for anthocyanin accumulation. In peach, QTLs for red plant organ traits map in an LG3 region with three MYB10 copies (PpMYB10.1, PpMYB10.2 and PpMYB10.3). In Japanese plum the gene copy number in this region differs with respect to peach: there are at least three copies of PsMYB10.1, with the expression of one of them (PsMYB10.1a) correlating with fruit skin color. The objective of this study was to determine a possible role of LG3-PsMYB10 genes in the natural variability of the flesh color trait and to develop a molecular marker for marker-assisted selection (MAS). We explored the variability within the LG3-PsMYB10 region using long-range sequences obtained in previous studies through CRISPR-Cas9 enrichment sequencing. We found that the PsMYB10.2 gene was only expressed in red flesh fruits. Its role in promoting anthocyanin biosynthesis was validated by transient overexpression in Japanese plum fruits. The analysis of long-range sequences identified an LTR retrotransposon in the promoter of the expressed PsMYB10.2 gene that explained the trait in 93.1% of the 145 individuals analyzed. We hypothesize that the LTR retrotransposon may promote the PsMYB10.2 expression and activate the anthocyanin biosynthesis pathway. We propose for the first time the PsMYB10.2 gene as candidate for the flesh color natural variation in Japanese plum and provide a molecular marker for MAS.

R2R3-MYB gene family: Genome-wide identification provides insight to improve the content of proanthocyanidins in Trifolium repens

The R2R3-MYB family is one of largest transcription factor families in plants playing significant roles in regulating anthocyanin and proanthocyanidin biosynthesis. Proanthocyanidins are one of major objectives to improve the quality of white clover (Trifolium repens L.), which have a beneficial effect on ruminant to prevent the lethal pasture bloat. A total of 133 TrR2R3-MYB genes were identified and distributed on all 16 chromosomes based on the whole genome information of white clover. Also, by exploring the gene structure, motifs and duplication events of TrR2R3-MYBs, as well as the evolutionary relationship with TrR2R3-MYB genes of other species, 10 TrR2R3-MYB genes with the potential to regulate the anthocyanins and proanthocyanidins biosynthesis were screened. These TrR2R3-MYB genes responded significantly to low temperature in white clover. In addition, they have different expression patterns in leaves, petioles and inflorescences of white clover. Importantly, TrMYB116 and TrMYB118 may positively regulate anthocyanin accumulation and low temperature response in white clover. TrMYB118 may also be associated with anthocyanin pigmentation pattern in Purple leaves. This study provides a basis for verifying the function of TrR2R3-MYB and breeding white clover cultivars with high proanthocyanidins.

Glucose Supply Induces PsMYB2-Mediated Anthocyanin Accumulation in Paeonia suffruticosa 'Tai Yang' Cut Flower

Tree peony (Paeonia suffruticosa) is a well-known Chinese ornamental plant with showy flower color. However, the color fading problem during vase time seriously blocks its development in the cut flower market. In this study, we found that exogenous glucose supply improved the color quality of P. suffruticosa 'Tai Yang' cut flowers with increased total soluble sugar and anthocyanin contents of petals. Besides, the promotion effect of glucose was better than the osmotic control of 3-O-methylglucose (3OMG) treatment and the glucose analog mannose treatment. The structural genes, including PsF3H, PsF3'H, PsDFR, PsAOMT, and PsUF5GT, were remarkably upregulated under glucose treatment. Meanwhile, the regulatory genes, including PsbHLH1, PsbHLH3, PsMYB2, PsWD40-1, and PsWD40-2, also showed a strong response to glucose treatment. Among these five regulatory genes, PsMYB2 showed less response to 3OMG treatment but was highly expressed under glucose and mannose treatments, indicating that PsMYB2 may have an important role in the glucose signal pathway. Ectopic overexpression of PsMYB2 in Nicotiana tabacum resulted in a strong pigmentation in petals and stamens of tobacco flowers accompanied with multiple anthocyanin biosynthetic genes upregulated. More importantly, the overexpression of PsMYB2 enhanced the ability of glucose-induced anthocyanin accumulation in Arabidopsis thaliana seedlings since PsMYB2-overexpressing Arabidopsis showed higher expression levels of AtPAL1, AtCHS, AtF3H, AtF3'H, AtDFR, and AtLDOX than those of wild type under glucose treatment. In summary, we suggested that glucose supply promoted petal coloration of P. suffruticosa 'Tai Yang' cut flower through the signal pathway, and PsMYB2 was a key component in this process. Our research made a further understanding of the mechanism that glucose-induced anthocyanin biosynthesis of P. suffruticosa cut flowers during postharvest development, laying a foundation for color retention technology development of cut flowers.

Eutrema EsMYB90 Gene Improves Growth and Antioxidant Capacity of Transgenic Wheat Under Salinity Stress

The ectopic expression of the EsMYB90 transcription factor gene from halophytic Eutrema salsugineum has been reported to enhance the level of anthocyanin and other flavonoid metabolites in transgenic tobacco. In this study, the wheat JW1 overexpressing EsMYB90 showed longer roots and higher fresh weight than that in wild type (WT) under salt stress. In addition, the transgenic wheat plants displayed significantly higher peroxidase (POD) and glutathione S-transferase (GST) activity, as well as markedly lower malondialdehyde (MDA) content than that of the WT during salt stress conditions. The analysis of histochemical staining and H₂O₂ level indicated that the accumulation of reactive oxygen species (ROS) was significantly lower in the roots of transgenic wheat plants compared to the WT under salt stress. Transcriptome analysis revealed that the EsMYB90 gene affected the expression of considerable amounts of stress-related genes that were involved in phenylpropanoid biosynthesis and antioxidant activity in transgenic plants subjected to NaCl treatment. Importantly, the significantly upregulated expression genes in transgenic wheat under salt stress were mainly associated with the antioxidative enzymes POD and GST encoding genes compared with the WT. Furthermore, EsMYB90 is suggested to bind with the MYB-binding elements of pTaANS2 and pTaDFR1 by dual luciferase assay, to activate the transcription of TaANS2 and TaDFR1 genes that are encoding key enzymes of anthocyanin biosynthesis in transgenic wheat plants. All the results indicated that, under salt stress, the EsMYB90 gene plays a crucial role in preventing wheat seedlings from oxidative stress damage via enhancing the accumulation of non-enzymatic flavonoids and activities of antioxidative enzymes, which suggested that EsMYB90 is an ideal candidate gene for the genetic engineering of crops.

Co-expression network analyses of anthocyanin biosynthesis genes in Ruellia (Wild Petunias; Acanthaceae)

Background

Anthocyanins are major pigments contributing to flower coloration and as such knowledge of molecular architecture underlying the anthocyanin biosynthetic pathway (ABP) is key to understanding flower color diversification. To identify ABP structural genes and associated regulatory networks, we sequenced 16 transcriptomes generated from 10 species of Ruellia and then conducted co-expression analyses among resulting data.

Results

Complete coding sequences for 12 candidate structural loci representing eight genes plus nine candidate regulatory loci were assembled. Analysis of non-synonymous/synonymous (dn/ds) mutation rates indicated all identified loci are under purifying selection, suggesting overall selection to prevent the accumulation of deleterious mutations. Additionally, upstream enzymes have lower rates of molecular evolution compared to downstream enzymes. However, site-specific tests of selection yielded evidence for positive selection at several sites, including four in F3'H2 and five in DFR3, and these sites are located in protein binding regions. A species-level phylogenetic tree constructed using a newly implemented hybrid transcriptome–RADseq approach implicates several flower color transitions among the 10 species. We found evidence of both regulatory and structural mutations to F3′5'H in helping to explain the evolution of red flowers from purple-flowered ancestors.

Conclusions

Sequence comparisons and co-expression analyses of ABP loci revealed that mutations in regulatory loci are likely to play a greater role in flower color transitions in Ruellia compared to mutations in underlying structural genes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01955-x.

A Myb transcription factor, PgMyb308-like, enhances the level of shikimate, aromatic amino acids, and lignins, but represses the synthesis of flavonoids and hydrolyzable tannins, in pomegranate (Punica granatum L.)

Pomegranate fruit peels are highly abundant in metabolites derived from the shikimate pathway, such as hydrolyzable tannins (HTs) and flavonoids. These metabolites are beneficial to human health (commercial juice is enriched with peel metabolites), and also protect the fruit from environmental stresses. To understand the transcriptional control of shikimate pathway-related metabolites in pomegranate, we cloned and characterized a subgroup S4 R2R3 Myb transcription factor, PgMyb308-like. Overexpressing PgMyb308-like in pomegranate hairy roots increased the accumulation of shikimate, aromatic amino acids, isoferulic acid, and total lignins, but led to reduced gallic acid and its downstream products HTs, as well as multiple flavonoids. Changes in these metabolites are supported by the increased expression of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase and shikimate dehydrogenase 1 (PgSDH1) (the SDH isoform associated with shikimate biosynthesis), and the reduced expression of PgSDH4 (the SDH isoform suggested to produce gallic acid). Transcriptome analysis of PgMyb308-like-overexpressing hairy roots further revealed reprogramming of cell wall-related genes, while overexpression of PgMyb308-like in Arabidopsis thaliana plants uncovered its distinct role in a different genetic and metabolic background. These results together suggest that PgMyb308-like activates genes in the shikimate pathway and lignin biosynthesis, but suppresses those involved in the production of HTs and flavonoids.

Expression of apple MdMYB10 transcription factor in sugar beet with a screenable marker role and antimicrobial activity

Selection of transgenic plants by using genes encoding screenable markers of plant origin with health benefit properties, such as anthocyanin is an important aim in plant genetic engineering. In this study, Malus domestica MYB10 (MdMYB10) gene, was used for Agrobacterium tumefaciens-mediated transformation of two SBS-02 and SBS-04 sugar beet lines. The impact of different light regimes on plant tissue culture from a combination of light, dark/light and dark was investigated. The results of this study showed that the MdMYB10 gene was successfully integrated into the selected purple transgenic lines, suggesting that the expression of MdMYB10 gene in sugar beet shoots can be used as a screenable markers for transformation, possibly replacing antibiotic resistant genes. Furthermore, the results of the antibacterial activity of transgenic plants extracts showed that the total extract obtained from transgenic lines significantly (P < 0.01) inhibited the growth and development of Enterococcus faecium and Enterococcus faecalis bacteria compared to the non-transgenic plants. The results of this study showed that the combination of betalain with vancomycin demonstrated a synergistic antimicrobial effect, also, suggesting that the expression of MdMYB10 may play a dual role by accumulating betalain and exhibiting a screenable markers function.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-022-03120-7.

Identification of a Strong Anthocyanin Activator, VbMYBA, From Berries of Vaccinium bracteatum Thunb

Wufanshu (Vaccinium bracteatum Thunb.), which is a wild member of the genus Vaccinium, accumulates high concentration of anthocyanin in its berries. In this study, the accumulated anthocyanins and their derivatives in Wufanshu berries were identified through UHPLC-MS/MS analysis. Candidate anthocyanin biosynthetic genes were identified from the transcriptome of Wufanshu berries. qRT-PCR analyses showed that the expression of anthocyanin structural genes correlated with anthocyanin accumulation in berries. The R2R3-MYB, VbMYBA, which is a homolog of anthocyanin promoting R2R3-MYBs from other Vaccinium species, was also identified. Transient expression of VbMYBA in Nicotiana tabacum leaves confirmed its role as an anthocyanin regulator, and produced a higher anthocyanin concentration when compared with blueberry VcMYBA expression. Dual-luciferase assays further showed that VbMYBA can activate the DFR and UFGT promoters from other Vaccinium species. VbMYBA has an additional 23 aa at the N terminus compared with blueberry VcMYBA, but this was shown not to affect the ability to regulate anthocyanins. Taken together, our results provide important information on the molecular mechanisms responsible for the high anthocyanin content in Wufanshu berries.

MYBA and MYBPA transcription factors co-regulate anthocyanin biosynthesis in blue-coloured berries

The regulatory network of R2R3 MYB transcription factors in anthocyanin biosynthesis is not fully understood in blue-coloured berries containing delphinidin compounds. We used blue berries of bilberry (Vaccinium myrtillus) to comprehensively characterise flavonoid-regulating R2R3 MYBs, which revealed a new type of co-regulation in anthocyanin biosynthesis between members of MYBA-, MYBPA1- and MYBPA2-subgroups. VmMYBA1, VmMYBPA1.1 and VmMYBPA2.2 expression was elevated at berry ripening and by abscisic acid treatment. Additionally, VmMYBA1 and VmMYBPA1.1 expression was strongly downregulated in a white berry mutant. Complementation and transient overexpression assays confirmed VmMYBA1 and VmMYBA2 to induce anthocyanin accumulation. Promoter activation assays showed that VmMYBA1, VmMYBPA1.1 and VmMYBPA2.2 had similar activity towards dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS), but differential regulation activity for UDP-glucose flavonoid 3-O-glucosyltransferase (UFGT) and flavonoid 3'5'-hydroxylase (F3'5'H) promoters. Silencing of VmMYBPA1.1 in berries led to the downregulation of key anthocyanin and delphinidin biosynthesis genes. Functional analyses of other MYBPA regulators, and a member of novel MYBPA3 subgroup, associated them with proanthocyanidin biosynthesis and F3'5'H expression. The existence of 18 flavonoid-regulating MYBs indicated gene duplication, which may have enabled functional diversification among MYBA, MYBPA1 and MYBPA2 subgroups. Our results provide new insights into the intricate regulation of the complex anthocyanin profile found in blue-coloured berries involving regulation of both cyanidin and delphinidin branches.

Anthocyanin synthesis potential in betalain-producing Caryophyllales plants

Although anthocyanins are widely distributed in higher plants, betalains have replaced anthocyanins in most species of the order Caryophyllales. The accumulation of flavonols in Caryophyllales plants implies that the late step of anthocyanin biosynthesis from dihydroflavonols to anthocyanins may be blocked in Caryophyllales. The isolation and characterization of functional dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS) from Caryophyllales plants has indicated a lack of anthocyanins due to suppression of DFR and ANS. In this study, we demonstrated that overexpression of DFR and ANS from Spinacia oleracea (SoDFR and SoANS, respectively) with PhAN9, which encodes glutathione S-transferase (required for anthocyanin sequestration) from Petunia induces ectopic anthocyanin accumulation in yellow tepals of the cactus Astrophytum myriostigma. A promoter assay of SoANS showed that the Arabidopsis MYB transcription factor PRODUCTION OF ANTHOCYANIN PIGMENT1 (PAP1) activated the SoANS promoter in Arabidopsis leaves. The overexpression of Arabidopsis transcription factors with PhAN9 also induced ectopic anthocyanin accumulation in yellow cactus tepals. PAP homologs from betalain-producing Caryophyllales did not activate the promoter of ANS. In-depth characterization of Caryophyllales PAPs and site-directed mutagenesis in the R2R3-MYB domains identified the amino acid residues affecting transactivation of Caryophyllales PAPs. The substitution of amino acid residues recovered the transactivation ability of Caryophyllales PAPs. Therefore, loss of function in MYB transcription factors may suppress expression of genes involved in the late stage of anthocyanin synthesis, resulting in a lack of anthocyanin in betalain-producing Caryophyllales plants.

Light Induced Regulation Pathway of Anthocyanin Biosynthesis in Plants

Anthocyanins are natural pigments with antioxidant effects that exist in various fruits and vegetables. The accumulation of anthocyanins is induced by environmental signals and regulated by transcription factors in plants. Numerous evidence has indicated that among the environmental factors, light is one of the most signal regulatory factors involved in the anthocyanin biosynthesis pathway. However, the signal transduction of light and molecular regulation of anthocyanin synthesis remains to be explored. Here, we focus on the research progress of signal transduction factors for positive and negative regulation in light-dependent and light-independent anthocyanin biosynthesis. In particular, we will discuss light-induced regulatory pathways and related specific regulators of anthocyanin biosynthesis in plants. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by transcription factors is discussed based on the significant progress.

Meta-analysis of the effect of expression of MYB transcription factor genes on abiotic stress

Background

MYB proteins are a large group of transcription factors. The overexpression of MYB genes has been reported to improve abiotic stress tolerance in plant. However, due to the variety of plant species studied and the types of gene donors/recipients, along with different experimental conditions, it is difficult to interpret the roles of MYB in abiotic stress tolerance from published data.

Methods

Using meta-analysis approach, we investigated the plant characteristics involved in cold, drought, and salt stress in MYB-overexpressing plants and analyzed the degrees of influence on plant performance by experimental variables.

Results

The results show that two of the four measured plant parameters in cold-stressed plants, two of the six in drought-stressed, and four of the 13 in salt-stressed were significantly impacted by MYB overexpression by 22% or more, and the treatment medium, donor/recipient species, and donor type significantly influence the effects of MYB-overexpression on drought stress tolerance. Also, the donor/recipient species, donor type, and stress duration all significantly affected the extent of MYB-mediated salt stress tolerance. In summary, this study compiles and analyzes the data across studies to help us understand the complex interactions that dictate the efficacy of heterologous MYB expression designed for improved abiotic stress tolerance in plants.

DkMYB14 is a bifunctional transcription factor that regulates the accumulation of proanthocyanidin in persimmon fruit

Proanthocyanidins (PAs) are phenolic secondary metabolites that contribute to the protection of plant and human health. Persimmon (Diospyros kaki Thunb.) can accumulate abundant PAs in fruit, which cause a strong sensation of astringency. Proanthocyanidins can be classified into soluble and insoluble PAs; the former cause astringency but the latter do not. Soluble PAs can be converted into insoluble PAs upon interacting with acetaldehydes. We demonstrate here that DkMYB14, which regulates the accumulation of PA in persimmon fruit flesh, is a bifunctional transcription factor that acts as a repressor in PA biosynthesis but becomes an activator when involved in acetaldehyde biosynthesis. Interestingly, both functions contribute to the elimination of astringency by decreasing PA biosynthesis and promoting its insolubilization. We show that the amino acid Gly39 in the R2 domain and the ethylene response factor-associated amphiphilic repression-like motif in the C-terminal of DkMYB14 are essential for the regulation of both PA and acetaldehyde synthesis. The repressive function of DkMYB14 was lost after the mutation of either motif, and all activities of DkMYB14 were eliminated following the mutation of both motifs. Our results demonstrate that DkMYB14 functions as both a transcriptional activator and a repressor, directly repressing biosynthesis of PA and promoting its insolubilization, resulting in non-astringency in persimmon.

A single amino acid substitution in the R2R3 conserved domain of the BrPAP1a transcription factor impairs anthocyanin production in turnip (Brassica rapa subsp. rapa)

The purple pigmentation in the epidermis of swollen roots of 'Tsuda' turnip (Brassica rapa subsp. rapa) is induced by light, providing a good system to investigate the genetic mechanism of light-dependent anthocyanin biosynthesis in B. rapa. Here, we identified the R2R3 MYB transcription factor gene PRODUCTION OF ANTHOCYANIN PIGMENT1 (BrPAP1a) as the critical gene in the anthocyanin-defective mutant w68. A nucleotide mutation in the turn region of the R3 domain was screened, which caused an amino acid substitution from glycine to serine (G94S). Functional analysis showed that the interaction of BrPAP1a with two bHLH factors ENHANCER OF GLABRA 3 (BrEGL3) and TRANSPARENT TESTA 8 (BrTT8) were impaired by the mutation. Expression of BrTT8 was activated by BrPAP1a and enhanced by MYB-bHLH-WDR (MBW) complexes, but blocked by the mutation. Furthermore, BrPAP1a directly bound the MYB-recognizing element (MRE) in the BrTT8 promoter, while the G94S substitution caused a loss of DNA-binding activity. Our findings indicate that G94 is required for protein interaction with BrTT8 and BrEGL3 and DNA-binding of BrPAP1a to activate BrTT8 expression, which leads to anthocyanin biosynthesis. Collectively, our data indicate the importance of the highly conserved amino acids within R2R3 MYB proteins in regulating anthocyanin biosynthesis and could aid programs to increase anthocyanins in turnip roots.

Genome-Wide Mining of MYB Transcription Factors in the Anthocyanin Biosynthesis Pathway of Gossypium Hirsutum

The MYB family, one of the largest transcription factor (TF) families, plays an important role in plant growth, development, and stress response. Although genome-wide analysis of the MYB family has been performed in many species based on sequence similarity, predicting the potential functions of the MYB genes and classifying the regulators into specific metabolic pathways remains difficult. In this study, using a hidden Markov model search and co-expression regulatory network analysis, we demonstrated a process to screen and identify potential MYB TFs in the anthocyanin biosynthesis pathway of Gossypium hirsutum. As a result, we identified 617 and 784 MYB genes (812 in total) from the previously reported and recently released genomes, respectively. Using 126 structural genes involved in the anthocyanin biosynthesis pathway as targets for several co-expression network analyses, we sorted out 31 R2R3-MYB genes, which are potential regulators in the specific pathway. Phylogenetic and collinearity analyses indicated that 83.9% of the 31 MYB genes originated from whole genome duplication or polyploidization. In addition, we revealed relatively specific regulatory relationships between the MYB TFs and their target structural genes. Approximately, 71% of the MYBs could regulate only a single anthocyanin-related structural gene. Moreover, we found that the A- and D- subgenome homoeologs of MYB TFs in G. hirsutum rarely co-regulate the same target gene. The current study not only demonstrated an easy method to rapidly predict potential TFs in a specific metabolic pathway, but also enhanced our understanding of the evolution, gene characteristics, expression, and regulatory pattern of MYB TFs in G. hirsutum.

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

Proanthocyanidins (PAs) are important phenolic compounds and PA biosynthesis is regulated by a ternary MBW complex consisting of a R2R3-MYB regulator, a bHLH factor and a WDR protein. In this study, a tobacco R2R3-MYB factor NtMYB330 was characterized as the PA-specific regulator in which the PA biosynthesis was promoted in the flowers of NtMYB330-overexpressing lines while decreased in the flowers of ntmyb330 mutants. NtMYB330 can interact with flavonoid-related bHLH partner NtAn1b and WDR protein NtAn11-1, and the NtMYB330-NtAn1b complex is required to achieve strong transcriptional activation of the PA-related structural genes NtDFR1, NtANS1, NtLAR1 and NtANR1. Our data reveal that NtMYB330 regulates PA biosynthesis in seeds and affects seed germination, in which NtMYB330-overexpressing lines showed higher PA accumulations in seed coats and inhibited germination, while ntmyb330 mutants had reduced seed coat PAs and improved germination. NtMYB330 affects seed germination possibly through two mechanisms: modulating seed coat PAs to affect coat-imposed dormancy. In addition, NtMYB330 regulates the expressions of abscisic acid (ABA) and gibberellin acid (GA) signaling-related genes, affecting ABA-GA crosstalk and seed germination. This study reveals that NtMYB330 specifically regulates PA biosynthesis via formation of the MBW complex in tobacco flowers and affects germination through adjustment of PA concentrations and ABA/GA signaling in tobacco seeds.

Transcriptomic Analysis of Root Restriction Effects on Phenolic Metabolites during Grape Berry Development and Ripening

In the present study, the effects of root restriction (RR) on the main phenolic metabolites and the related gene expression at different developmental stages were studied at the transcriptomic and metabolomic levels in "Summer Black" grape berries (Vitis vinifera × Vitis labrusca). The results were as follows: seven phenolic acid compounds, three stilbene compounds, nine flavonol compounds, 10 anthocyanin compounds, and 24 proanthocyanidin compounds were identified by ultra-performance liquid chromatography-high-resolution mass spectrometry. RR treatment significantly promoted the biosynthesis of phenolic acid, trans-resveratrol, flavonol, and anthocyanin and also affected the proanthocyanidin content, which was elevated in the early developmental stages and then reduced in the late developmental stages. The functional genes for phenylalanine ammonia-lyase, trans-cinnamate 4-monooxygenase, 4-coumarate-CoA ligase, shikimate O-hydroxycinnamoyl transferase, chalcone synthase, chalcone isomerase, stilbene synthase, flavonoid 3',5'-hydroxylase, anthocyanidin 3-O-glucosyltransferase, and the transcription factors MYBA1, MYBA2, MYBA3, and MYBA22 were inferred to play critical roles in the changes regulated by RR treatment.

Identification of the Eutrema salsugineum EsMYB90 gene important for anthocyanin biosynthesis

BACKGROUND

Anthocyanins contribute to coloration and antioxidation effects in different plant tissues. MYB transcription factors have been demonstrated to be a key regulator for anthocyanin synthesis in many plants. However, little information was available about the MYB genes in the halophyte species Eutrema salsugineum.

RESULT

Here we report the identification of an important anthocyanin biosynthesis regulator EsMYB90 from Eutrema salsugineum, which is a halophyte tolerant to multiple abiotic stresses. Our phylogenetic and localization analyses supported that EsMYB90 is an R2R3 type of MYB transcription factor. Ectopic expression of EsMYB90 in tobacco and Arabidopsis enhanced pigmentation and anthocyanin accumulation in various organs. The transcriptome analysis revealed that 42 genes upregulated by EsMYB90 in 35S:EsMYB90 tobacco transgenic plants are required for anthocyanin biosynthesis. Moreover, our qRT-PCR results showed that EsMYB90 promoted expression of early (PAL, CHS, and CHI) and late (DFR, ANS, and UFGT) anthocyanin biosynthesis genes in stems, leaves, and flowers of 35S:EsMYB90 tobacco transgenic plants.

CONCLUSIONS

Our results indicated that EsMYB90 is a MYB transcription factor, which regulates anthocyanin biosynthesis genes to control anthocyanin biosynthesis. Our work provides a new tool to enhance anthocyanin production in various plants.

Identification of the Eutrema salsugineum EsMYB90 gene important for anthocyanin biosynthesis

BACKGROUND

Anthocyanins contribute to coloration and antioxidation effects in different plant tissues. MYB transcription factors have been demonstrated to be a key regulator for anthocyanin synthesis in many plants. However, little information was available about the MYB genes in the halophyte species Eutrema salsugineum.

RESULT

Here we report the identification of an important anthocyanin biosynthesis regulator EsMYB90 from Eutrema salsugineum, which is a halophyte tolerant to multiple abiotic stresses. Our phylogenetic and localization analyses supported that EsMYB90 is an R2R3 type of MYB transcription factor. Ectopic expression of EsMYB90 in tobacco and Arabidopsis enhanced pigmentation and anthocyanin accumulation in various organs. The transcriptome analysis revealed that 42 genes upregulated by EsMYB90 in 35S:EsMYB90 tobacco transgenic plants are required for anthocyanin biosynthesis. Moreover, our qRT-PCR results showed that EsMYB90 promoted expression of early (PAL, CHS, and CHI) and late (DFR, ANS, and UFGT) anthocyanin biosynthesis genes in stems, leaves, and flowers of 35S:EsMYB90 tobacco transgenic plants.

CONCLUSIONS

Our results indicated that EsMYB90 is a MYB transcription factor, which regulates anthocyanin biosynthesis genes to control anthocyanin biosynthesis. Our work provides a new tool to enhance anthocyanin production in various plants.

MYB Transcription Factors as Regulators of Secondary Metabolism in Plants

MYB transcription factors (TFs), as one of the largest gene families in plants, play important roles in multiple biological processes, such as plant growth and development, cell morphology and pattern building, physiological activity metabolism, primary and secondary metabolic reactions, and responses to environmental stresses. The function of MYB TFs in crops has been widely studied, but few studies have been done on medicinal plants. In this review, we summarized the MYB TFs that play important roles in secondary metabolism and emphasized the possible mechanisms underlying how MYB TFs are regulated at the protein, posttranscriptional, and transcriptional levels, as well as how they regulate the downstream target gene networks related to secondary metabolism in plants, especially in medicinal plants.

Alternative Splicing in the Anthocyanin Fruit Gene Encoding an R2R3 MYB Transcription Factor Affects Anthocyanin Biosynthesis in Tomato Fruits

Tomato (Solanum lycopersicum) fruits are typically red at ripening, with high levels of carotenoids and a low content in flavonoids. Considerable work has been done to enrich the spectrum of their health-beneficial phytochemicals, and interspecific crosses with wild species have successfully led to purple anthocyanin-colored fruits. The Aft (Anthocyanin fruit) tomato accession inherited from Solanum chilense the ability to accumulate anthocyanins in fruit peel through the introgression of loci controlling anthocyanin pigmentation, including four R2R3 MYB transcription factor-encoding genes. Here, we carried out a comparative functional analysis of these transcription factors in wild-type and Aft plants, and tested their ability to take part in the transcriptional complexes that regulate the biosynthetic pathway and their efficiency in inducing anthocyanin pigmentation. Significant differences emerged for SlAN2like, both in the expression level and protein functionality, with splicing mutations determining a complete loss of function of the wild-type protein. This transcription factor thus appears to play a key role in the anthocyanin fruit pigmentation. Our data provide new clues to the long-awaited genetic basis of the Aft phenotype and contribute to understand why domesticated tomato fruits display a homogeneous red coloration without the typical purple streaks observed in wild tomato species.

Effects on Plant Growth and Reproduction of a Peach R2R3-MYB Transcription Factor Overexpressed in Tobacco

In plants, anthocyanin production is controlled by MYB and bHLH transcription factors. In peach, among the members of these families, MYB10.1 and bHLH3 have been shown to be the most important genes for production of these pigments during fruit ripening. Anthocyanins are valuable molecules, and the overexpression of regulatory genes in annual fast-growing plants has been explored for their biotechnological production. The overexpression of peach MYB10.1 in tobacco plants induced anthocyanin pigmentation, which was particularly strong in the reproductive parts. Pigment production was the result of an up-regulation of the expression level of key genes of the flavonoid biosynthetic pathway, such as NtCHS, NtCHI, NtF3H, NtDFR, NtANS, and NtUFGT, as well as of the proanthocyanidin biosynthetic pathway such as NtLAR. Nevertheless, phenotypic alterations in transgenic tobacco lines were not only limited to anthocyanin production. Lines showing a strong phenotype (type I) exhibited irregular leaf shape and size and reduced plant height. Moreover, flowers had reduced length of anther's filament, nondehiscent anthers, reduced pistil length, aborted nectary glands, and impaired capsule development, but the reproductive parts including androecium, gynoecium, and petals were more pigmented that in wild type. Surprisingly, overexpression of peach MYB10.1 led to suppression of NtMYB305, which is required for floral development and, of one of its target genes, NECTARIN1 (NtNCE1), involved in the nectary gland formation. MYB10.1 overexpression up-regulated JA biosynthetic (NtAOS) and signaling (NtJAZd) genes, as well as 1-aminocyclopropane-1-carboxylate oxidase (NtACO) in flowers. The alteration of these hormonal pathways might be among the causes of the observed floral abnormalities with defects in both male and female gametophyte development. In particular, approximately only 30% of pollen grains of type I lines were viable, while during megaspore formation, there was a block during FG1 (St3-II). This block seemed to be associated to an excessive accumulation of callose. It can be concluded that the overexpression of peach MYB10.1 in tobacco not only regulates flavonoid biosynthesis (anthocyanin and proanthocyanidin) in the reproductive parts but also plays a role in other processes such as vegetative and reproductive development.

R2R3-MYB transcription factor MYB6 promotes anthocyanin and proanthocyanidin biosynthesis but inhibits secondary cell wall formation in Populus tomentosa

The secondary cell wall is an important carbon sink in higher plants and its biosynthesis requires coordination of metabolic fluxes in the phenylpropanoid pathway. In Arabidopsis (Arabidopsis thaliana), MYB75 and the KNOX transcription factor KNAT7 form functional complexes to regulate secondary cell wall formation in the inflorescence stem. However, the molecular mechanism by which these transcription factors control different branches of the phenylpropanoid pathway remains poorly understood in woody species. We isolated an R2R3-MYB transcription factor MYB6 from Populus tomentosa and determined that it was expressed predominately in young leaves. Overexpression of MYB6 in transgenic poplar upregulated flavonoid biosynthetic gene expression, resulting in significantly increased accumulation of anthocyanin and proanthocyanidins. MYB6-overexpression plants showed reduced secondary cell wall deposition, accompanied by repressed expression of secondary cell wall biosynthetic genes. We further showed that MYB6 interacted physically with KNAT7 and formed functional complexes that acted to repress secondary cell wall development in poplar and Arabidopsis. The results provide an insight into the transcriptional mechanisms involved in the regulation of the metabolic fluxes between the flavonoid and lignin biosynthetic pathways in poplar.

Assessing Anthocyanin Biosynthesis in Solanaceae as a Model Pathway for Secondary Metabolism

Solanaceae have played an important role in elucidating how flower color is specified by the flavonoid biosynthesis pathway (FBP), which produces anthocyanins and other secondary metabolites. With well-established reverse genetics tools and rich genomic resources, Solanaceae provide a robust framework to examine the diversification of this well-studied pathway over short evolutionary timescales and to evaluate the predictability of genetic perturbation on pathway flux. Genomes of eight Solanaceae species, nine related asterids, and four rosids were mined to evaluate variation in copy number of the suite of FBP enzymes involved in anthocyanin biosynthesis. Comparison of annotation sources indicated that the NCBI annotation pipeline generated more and longer FBP annotations on average than genome-specific annotation pipelines. The pattern of diversification of each enzyme among asterids was assessed by phylogenetic analysis, showing that the CHS superfamily encompasses a large paralogous family of ancient and recent duplicates, whereas other FBP enzymes have diversified via recent duplications in particular lineages. Heterologous expression of a pansy F3′5′H gene in tobacco changed flower color from pink to dark purple, demonstrating that anthocyanin production can be predictably modified using reverse genetics. These results suggest that the Solanaceae FBP could be an ideal system to model genotype-to-phenotype interactions for secondary metabolism.

The WRKY transcription factor GhWRKY27 coordinates the senescence regulatory pathway in upland cotton (Gossypium hirsutum L.)

BACKGROUND

Premature senescence can reduce the yield and quality of crops. WRKY transcription factors (TFs) play important roles during leaf senescence, but little is known about their ageing mechanisms in cotton.

RESULTS

In this study, a group III WRKY TF, GhWRKY27, was isolated and characterized. The expression of GhWRKY27 was induced by leaf senescence and was higher in an early-ageing cotton variety than in a non-early-ageing cotton variety. Overexpression of GhWRKY27 in Arabidopsis promoted leaf senescence, as determined by reduced chlorophyll content and elevated expression of senescence-associated genes (SAGs). Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that GhWRKY27 interacted with an MYB TF, GhTT2. Putative target genes of GhWRKY27 were identified via chromatin immunoprecipitation followed by sequencing (ChIP-seq). Yeast one-hybrid (Y1H) assay and electrophoretic mobility shift assay (EMSA) revealed that GhWRKY27 binds directly to the promoters of cytochrome P450 94C1 (GhCYP94C1) and ripening-related protein 2 (GhRipen2-2). In addition, the expression patterns of GhTT2, GhCYP94C1 and GhRipen2-2 were identified during leaf senescence. Transient dual-luciferase reporter assay indicated that GhWRKY27 could activate the expression of GhCYP94C1 and GhRipen2-2.

CONCLUSIONS

Our work lays the foundation for further study of the functional roles of WRKY genes during leaf senescence in cotton. In addition, our data provide new insights into the senescence-associated mechanisms of WRKY genes in cotton.

Activator-type R2R3-MYB genes induce a repressor-type R2R3-MYB gene to balance anthocyanin and proanthocyanidin accumulation

Anthocyanin and proanthocyanidin (PA) accumulation is regulated by both myeloblastosis (MYB) activators and repressors, but little information is available on hierarchical interactions between the positive and negative regulators. Here, we report on a R2R3-MYB repressor in peach, designated PpMYB18, which acts as a negative regulator of anthocyanin and PA accumulation. PpMYB18 can be activated by both anthocyanin- and PA-related MYB activators, and is expressed both at fruit ripening and juvenile stages when anthocyanins or PAs, respectively, are being synthesized. The PpMYB18 protein competes with MYB activators for binding to basic Helix Loop Helixes (bHLHs), which develops a fine-tuning regulatory loop to balance PA and anthocyanin accumulation. In addition, the bHLH binding motif in the R3 domain and the C1 and C2 repression motifs in the C-terminus of PpMYB18 both confer repressive activity of PpMYB18. Our study also demonstrates a modifying negative feedback loop, which prevents cells from excess accumulation of anthocyanin and PAs, and serves as a model for balancing secondary metabolite accumulation at the transcriptional level.

Evolutionary Analysis of MBW Function by Phenotypic Rescue in Arabidopsis thaliana

The MBW complex consisting of the three proteins R2R3MYB, bHLH and WDR regulates five traits in Arabidopsis thaliana including trichome and root hair patterning, seed coat color, anthocyanidin production and seed coat mucilage release. The WDR gene TTG1 regulates each trait in specific combinations with different bHLH and R2R3MYB proteins. In this study we analyze to what extent the biochemical properties of the MBW proteins contribute to trait specificity by expressing them in appropriate A. thaliana mutants. We show that the rescue behavior of A. thaliana bHLH and R2R3MYB protein is sufficient to explain the function as derived previously from mutant analysis. When extending this rescue approach using MBW proteins from other species we find that proteins involved in anthocyanidin regulation typically show a rescue of the anthocyanidin phenotype but not of the other traits. Finally, we correlate the rescue abilities of MBW protein from different species with the A. thaliana proteins.

Transcriptomic analysis of Lycium ruthenicum Murr. during fruit ripening provides insight into structural and regulatory genes in the anthocyanin biosynthetic pathway

Fruit development in Lycium ruthenicum Murr. involves a succession of physiological and biochemical changes reflecting the transcriptional modulation of thousands of genes. Although recent studies have investigated the dynamic transcriptomic responses during fruit ripening in L. ruthenicum, most have been limited in scope, and thus systematic data representing the structural genes and transcription factors involved in anthocyanin biosynthesis are lacking. In this study, the transcriptomes of three ripening stages associated with anthocyanin accumulation, including S1 (green ripeness stage), S2 (skin color change) and S3 (complete ripeness stage) in L. ruthenicum were investigated using Illumina sequencing. Of a total of 43,573 assembled unigenes, 12,734 were differentially expressed during fruit ripening in L. ruthenicum. Twenty-five significantly differentially expressed structural genes (including PAL, C4H, 4CL, CHS, CHI, F3H, F3'H, F3'5'H, DFR, ANS and UFGT) were identified that might be associated with anthocyanin biosynthesis. Additionally, several transcription factors, including MYB, bHLH, WD40, NAC, WRKY, bZIP and MADS, were correlated with the structural genes, implying their important interaction with anthocyanin biosynthesis-related genes. Our findings provide insight into anthocyanin biosynthesis and regulation patterns in L. ruthenicum and offer a systematic basis for elucidating the molecular mechanisms governing anthocyanin biosynthesis in L. ruthenicum.

NbGIS regulates glandular trichome initiation through GA signaling in tobacco

KEY MESSAGE

A novel gene NbGIS positively regulates glandular trichome initiation through GA Signaling in tobacco. NbMYB123-like regulates glandular trichome initiation by acting downstream of NbGIS in tobacco. Glandular trichome is a specialized multicellular structure which has capability to synthesize and secrete secondary metabolites and protects plants from biotic and abiotic stresses. Our previous results revealed that a C2H2 zinc-finger transcription factor GIS and its sub-family genes act upstream of GL3/EGL3-GL1-TTG1 transcriptional activator complex to regulate trichome initiation in Arabidopsis. In this present study, we found that NbGIS could positively regulate glandular trichome development in Nicotiana benthamiana (tobacco). Our result demonstrated that 35S:NbGIS lines exhibited much higher densities of trichome on leaves, main stems, lateral branches and sepals than WT plants, while NbGIS:RNAi lines had the opposite phenotypes. Furthermore, our results also showed that NbGIS was required in response to GA signal to control glandular trichome initiation in Nicotiana benthamiana. In addition, our results also showed that NbGIS significantly influenced GA accumulation and expressions of marker genes of the GA biosynthesis, might result in the changes of growth and maturation in tobacco. Lastly, our results also showed that NbMYB123-like regulated glandular trichome initiation in tobacco by acting downstream of NbGIS. These findings provide new insights to discover the molecular mechanism by which C2H2 transcriptional factors regulates glandular trichome initiation through GA signaling pathway in tobacco.

Two amino acid changes in the R3 repeat cause functional divergence of two clustered MYB10 genes in peach

R2R3-MYB genes play a pivotal role in regulating anthocyanin accumulation. Here, we report two tandemly duplicated R2R3-MYB genes in peach, PpMYB10.1 and PpMYB10.2, with the latter showing lower ability to induce anthocyanin accumulation than the former. Site-directed mutation assay revealed two amino acid changes in the R3 repeat, Arg/Lys⁶⁶ and Gly/Arg⁹³, responsible for functional divergence between these two PpMYB10 genes. Anthocyanin-promoting activity of PpMYB10.2 was significantly increased by a single amino acid replacement of Arg⁹³ with Gly⁹³. However, either the Gly⁹³ → Arg⁹³ or Arg⁶⁶ → Lys⁶⁶ substitutions alone showed little impact on anthocyanin-promoting activity of PpMYB10.1, but simultaneous substitutions caused a significant decrease. Reciprocal substitution of Arg/Gly⁹³ could significantly alter binding affinity to PpbHLH3, while the Arg⁶⁶ → Lys⁶⁶ substitution is predicted to affect the folding of the MYB DNA-binding domain, instead of PpbHLH3-binding affinity. Overall, the change of anthocyanin-promoting activity was accompanied with that of bHLH-binding affinity, suggesting that DNA-binding affinity of R2R3-MYBs depends on their bHLH partners. Our study is helpful for understanding of functional evolution of R2R3-MYBs and their interaction with DNA targets.

Metabolic Flux Enhancement and Transcriptomic Analysis Displayed the Changes of Catechins Following Long-Term Pruning in Tea Trees ( Camellia sinensis)

The tea tree is a perennial woody plant, and pruning is one of the most crucial cultivation measurements for tea plantation management. To date, the relationship between long-term pruning and metabolic flux enhancement in tea trees has not been studied. In this research, 11-year-old pruned tea trees from four different cultivars were randomly selected for transcriptome analysis and characteristic secondary metabolite analysis together with controls. The findings revealed that epigallocatechin gallate (EGCG) accumulation in pruned tea trees was significantly higher than that in unpruned tea trees. SCPL1A expression (encoding a class of serine carboxypeptidase), which has been reported to have a catalytic ability during EGCG biosynthesis, together with LAR, encoding leucoanthocyanidin reductase, was upregulated in the pruned tea trees. Moreover, metabolic flux enhancement and transcriptome analysis revealed low EGCG accumulation in the leaves of unpruned tea trees. Because of the bitter and astringent taste of EGCG, these results provide a certain understanding to the lower bitterness and astringency in teas from "ancient tea trees", growing in the wild with no trimming, than teas produced from pruned plantation trees.

MYBs Drive Novel Consumer Traits in Fruits and Vegetables

Eating plant-derived compounds can lead to a longer and healthier life and also benefits the environment. Innovation in the fresh food sector, as well as new cultivars, can improve consumption of fruit and vegetables, with MYB transcription factors being a target to drive this novelty. Plant MYB transcription factors are implicated in diverse roles including development, hormone signalling, and metabolite biosynthesis. The reds and blues of fruit and vegetables provided by anthocyanins, phlobaphenes, and betalains are controlled by specific R2R3 MYBs. New studies are now revealing that MYBs also control carotenoid biosynthesis and other quality traits, such as flavour and texture. Future breeding techniques may manipulate or create alleles of key MYB transcription factors.

The zinc-finger transcription factor ZAT6 is essential for hydrogen peroxide induction of anthocyanin synthesis in Arabidopsis

The accumulation of flavonoids is activated by various abiotic stresses, and the induction of reactive oxygen species (ROS) especially hydrogen peroxide (H₂O₂) is a general response to abiotic stress in plants. However, the direct link between flavonoids and H₂O₂ and underlying mechanism remain elusive. In this study, we found that the concentrations of anthocyanin and flavonoids were significantly induced by H₂O₂ treatment. Furthermore, we found that the transcript level of ZINC FINGER of ARABIDOPSIS THALIANA 6 (ZAT6) was significantly activated after exogenous H₂O₂ treatment, and modulation of AtZAT6 expression positively affected the concentrations of both anthocyanin and total flavonoids. Notably, exogenous H₂O₂-induced anthocyanin synthesis was largely alleviated in AtZAT6 knockdown plants, but showed higher level in AtZAT6 overexpressing plants. AtZAT6 directly activated the expressions of TT5, TT7, TT3, TT18, MYB12, and MYB111 through binding to their promoters with TACAAT elements of these genes, and the activation of MYB12 and MYB111 up-regulated the expressions of TT4 and TT6. Taken together, this study indicates that AtZAT6 plays important role in H₂O₂-activated anthocyanin synthesis, via directly binding to the promoters of several genes that involved in anthocyanin synthesis.

Fine Mapping Identifies SmFAS Encoding an Anthocyanidin Synthase as a Putative Candidate Gene for Flower Purple Color in Solanum melongena L

Anthocyanins are the main pigments in flowers and fruits. These pigments are responsible for the red, red-purple, violet, and purple color in plants, and act as insect and animal attractants. In this study, phenotypic analysis of the purple flower color in eggplant indicated that the flower color is controlled by a single dominant gene, FAS. Using an F₂ mapping population derived from a cross between purple-flowered 'Blacknite' and white-flowered 'Small Round', FlowerAnthocyanidin Synthase (FAS) was fine mapped to an approximately 165.6-kb region between InDel marker Indel8-11 and Cleaved Amplified Polymorphic Sequences (CAPS) marker Efc8-32 on Chromosome 8. On the basis of bioinformatic analysis, 29 genes were subsequently located in the FAS target region, among which were two potential Anthocyanidin Synthase (ANS) gene candidates. Allelic sequence comparison results showed that one ANS gene (Sme2.5_01638.1_g00003.1) was conserved in promoter and coding sequences without any nucleotide change between parents, whereas four single-nucleotide polymorphisms were detected in another ANS gene (Sme2.5_01638.1_g00005.1). Crucially, a single base pair deletion at site 438 resulted in premature termination of FAS, leading to the loss of anthocyanin accumulation. In addition, FAS displayed strong expression in purple flowers compared with white flowers and other tissues. Collectively, our results indicate that Sme2.5_01638.1_g00005.1 is a good candidate gene for FAS, which controls anthocyanidin synthase in eggplant flowers. The present study provides information for further potential facilitate genetic engineering for improvement of anthocyanin levels in plants.

An R2R3-MYB transcription factor, OjMYB1, functions in anthocyanin biosynthesis in Oenanthe javanica

This study showed that an R2R3-MYB transcription factor, OjMYB1, is involved in anthocyanin biosynthesis and accumulation in Oenanthe javanica. Anthocyanins can be used as safe natural food colorants, obtained from many plants. R2R3-MYB transcription factors (TFs) play important roles in anthocyanins biosynthesis during plant development. Oenanthe javanica is a popular vegetable with high nutritional values and numerous medical functions. O. javanica has purple petioles that are mainly due to anthocyanins accumulation. In the present study, the gene encoding an R2R3-MYB TF, OjMYB1, was isolated from purple O. javanica. Sequencing results showed that OjMYB1 contained a 912-bp open reading frame encoding 303 amino acids. Sequence alignments revealed that OjMYB1 contained bHLH-interaction motif ([DE]Lx2[RK]x3Lx6Lx3R) and ANDV motif ([A/G]NDV). Phylogenetic analysis indicated that the OjMYB1 classified into the anthocyanins biosynthesis clade. Subcellular localization assay showed that OjMYB1 was a nuclear protein in vivo. The heterologous expression of OjMYB1 in Arabidopsis could enhance the anthocyanins content and up-regulate the expression levels of the structural genes-related anthocyanins biosynthesis. Yeast two-hybrid assay indicated that OjMYB1 could interact with AtTT8 and AtEGL3 proteins. Enzymatic analysis revealed that overexpression of OjMYB1 gene up-regulated the enzyme activity of 3-O-glycosyltransferase encoded by AtUGT78D2 in transgenic Arabidopsis. Our results provided a comprehensive understanding of the structure and function of OjMYB1 TF in O. javanica.

Isolation and Characterization of the Flavonol Regulator CcMYB12 From the Globe Artichoke [Cynara cardunculus var. scolymus (L.) Fiori]

Flavonoids are a well-studied group of secondary metabolites, belonging to the phenylpropanoid pathway. Flavonoids are known to exhibit health promoting effects such as antioxidant capacities, anti-cancer and anti-inflammatory activity. Globe artichoke is an important source of bioactive phenolic compounds, including flavonoids. To study the regulation of their biosynthesis, a R2R3-MYB transcription factor, CcMYB12, was isolated from artichoke leaves. Phylogenetic analysis showed that this protein belongs to the MYB subgroup 7 (flavonol-specific MYB), which includes Arabidopsis AtMYB12, grapevine VvMYBF1, and tomato SlMYB12. CcMYB12 transcripts were detected specifically in artichoke immature inflorescence and young leaves and overlapped with the profiles of flavonol biosynthetic genes. Electrophoretic mobility shift assays (EMSAs) revealed that recombinant CcMYB12 protein is able to bind to ACII element, a DNA binding site ubiquitously present in the promoters of genes encoding flavonol biosynthetic enzymes. In transgenic Arabidopsis plants, the overexpression of CcMYB12 activated the expression of endogenous flavonol biosynthesis genes, leading to an increase of flavonol accumulation and a decrease of anthocyanins in leaves. Likewise, in transgenic tobacco petals and leaves, the overexpression of CcMYB12 decreased anthocyanin levels and increased flavonols.

TRANSPARENT TESTA GLABRA 1-Dependent Regulation of Flavonoid Biosynthesis

The flavonoid composition of various tissues throughout plant development is of biological relevance and particular interest for breeding. Arabidopsis thaliana TRANSPARENT TESTA GLABRA 1 (AtTTG1) is an essential regulator of late structural genes in flavonoid biosynthesis. Here, we provide a review of the regulation of the pathway's core enzymes through AtTTG1-containing R2R3-MYELOBLASTOSIS-basic HELIX-LOOP-HELIX-WD40 repeat (MBW(AtTTG1)) complexes embedded in an evolutionary context. We present a comprehensive collection of A. thalianattg1 mutants and AtTTG1 orthologs. A plethora of MBW(AtTTG1) mechanisms in regulating the five major TTG1-dependent traits is highlighted.

Molecular analysis of anthocyanin-related genes in ornamental cabbage

Ornamental cabbage (Brassica oleracea var. acephala) is a winter-grown and important decorative plant of the family Brassicaceae, which displays an exceptional coloration in the central leaves of the rosette. Anthocyanins are the key determinant of the red, purple, and blue colors of vegetative and reproductive parts of many plant species including ornamental cabbage. Total anthocyanin content was measured spectrophotometrically, and the highest anthocyanin content was detected in the red followed by light-red and white ornamental cabbage lines. Anthocyanin biosynthesis is controlled by members of three different transcription factor (TF) families, such as MYB, basic helix-loop-helix (bHLH), and WD40 repeats (WDR), which function as a MBW complex. We identified three MYB, six bHLH, and one WDR TFs that regulate anthocyanin biosynthesis in ornamental cabbage. The expression of the regulatory and biosynthetic genes for anthocyanin synthesis was determined by qPCR. The tested structural genes of the anthocyanin pathway were shown to be up-regulated in the red followed by light-red ornamental cabbage lines; however, the expression levels of the late biosynthetic genes were barely detected in the white ornamental cabbage lines. Among the regulatory genes, BoPAP2 (MYB), BoTT8, BoEGL3.1, and BoMYC1.2 (bHLH), and BoTTG1 (WDR) were identified as candidates for the regulation of anthocyanin biosynthesis. This work could be useful for the breeding of novel colorful ornamental cabbage cultivars.

Multiple Copies of a Simple MYB-Binding Site Confers Trans-regulation by Specific Flavonoid-Related R2R3 MYBs in Diverse Species

In apple, the MYB transcription factor MYB10 controls the accumulation of anthocyanins. MYB10 is able to auto-activate its expression by binding its own promoter at a specific motif, the R1 motif. In some apple accessions a natural mutation, termed R6, has more copies of this motif within the MYB10 promoter resulting in stronger auto-activation and elevated anthocyanins. Here we show that other anthocyanin-related MYBs selected from apple, pear, strawberry, petunia, kiwifruit and Arabidopsis are able to activate promoters containing the R6 motif. To examine the specificity of this motif, members of the R2R3 MYB family were screened against a promoter harboring the R6 mutation. Only MYBs from subgroups 5 and 6 activate expression by binding the R6 motif, with these MYBs sharing conserved residues in their R2R3 DNA binding domains. Insertion of the apple R6 motif into orthologous promoters of MYB10 in pear (PcMYB10) and Arabidopsis (AtMY75) elevated anthocyanin levels. Introduction of the R6 motif into the promoter region of an anthocyanin biosynthetic enzyme F3'5'H of kiwifruit imparts regulation by MYB10. This results in elevated levels of delphinidin in both tobacco and kiwifruit. Finally, an R6 motif inserted into the promoter the vitamin C biosynthesis gene GDP-L-Gal phosphorylase increases vitamin C content in a MYB10-dependent manner. This motif therefore provides a tool to re-engineer novel MYB-regulated responses in plants.

Identification and Characterization of Anthocyanin Biosynthesis-Related Genes in Kohlrabi

Kohlrabi (Brassica oleracea var. gongylodes L.) is an important vegetable of the Brassicaceae family. The main edible part of kohlrabi is the swollen stem. The purple cultivars make anthocyanin mainly in the peel of the swollen stem, while in the leaf, it is limited to the midrib, but green cultivars do not. Anthocyanins are advantageous for both plants as well as humans. Two anthocyanin compounds were detected by high pressure liquid chromatography (HPLC) only in the peel of the purple kohlrabi cultivar. Three MYBs, three bHLHs, and one WD40 TF were identified as the candidate regulatory genes in kohlrabi. There was an abundance of transcript levels for the late biosynthetic genes more specifically for BoF3'H, BoDFR, BoLDOX, and BoGST in the purple peel while scarcely detectable in other tissues for both cultivars. The expression of BoPAP2 and BoTT8 was higher in the peel of the purple cultivar than the green cultivar. The expression of BoMYBL2.2 orthologue of Arabidopsis MYBL2, a negative regulator of anthocyanins, was dramatically decreased in the purple peel. The expression of BoACO1, a key gene for ethylene biosynthesis, and BoNCED3, an important gene of the ABA pathway, was down- and upregulated, respectively, in the peel of purple kohlrabi.

SmMYB36, a Novel R2R3-MYB Transcription Factor, Enhances Tanshinone Accumulation and Decreases Phenolic Acid Content in Salvia miltiorrhiza Hairy Roots

Phenolic acids and tanshinones are two major bioactive components in Salvia miltiorrhiza Bunge. A novel endogenous R2R3-MYB transcription factor, SmMYB36, was identified in this research. This transcript factor can simultaneously influence the content of two types of components in SmMYB36 overexpression hairy roots. SmMYB36 was mainly localized in the nucleus of onion epidermis and it has transactivation activity. The overexpression of SmMYB36 promoted tanshinone accumulation but inhibited phenolic acid and flavonoid biosynthesis in Salvia miltiorrhiza hairy roots. The altered metabolite content was due to changed metabolic flow which was regulated by transcript expression of metabolic pathway genes. The gene transcription levels of the phenylpropanoid general pathway, tyrosine derived pathway, methylerythritol phosphate pathway and downstream tanshinone biosynthetic pathway changed significantly due to the overexpression of SmMYB36. The wide distribution of MYB binding elements (MBS, MRE, MBSI and MBSII) and electrophoretic mobility shift assay results indicated that SmMYB36 may be an effective tool to regulate metabolic flux shifts.