StMYB44 negatively regulates anthocyanin biosynthesis at high temperatures in tuber flesh of potato

Tuber transcriptome analysis reveals a novel WRKY transcription factor StWRKY70 potentially involved in potato pigmentation

Tuber flesh pigmentation, conferred by the presence of secondary metabolite anthocyanins, is one of many key agronomic traits for potato tubers. Although several genes of potato anthocyanin biosynthesis have been reported, transcription factors (TFs) contributing to tuber flesh pigmentation are still not fully understood. In this study, transcriptomic profiling of diploid potato accessions with or without tuber flesh pigmentation was conducted and genes of the anthocyanin biosynthesis pathway were found significantly enriched within the 1435 differentially expressed genes (DEGs). Weighted Gene Co-expression Network Analysis (WGCNA) and connectivity analysis pinpointed a subset of 173 genes closely related to the key biosynthetic gene StDFR. Of the eight transcription factors in the subset, group III WRKY StWRKY70, was chosen for showing high connectivity to StDFR and ten other anthocyanin biosynthetic genes and homology to known WRKYs of anthocyanin pathway. The transient activation assay showed StWRKY70 predominantly stimulated the expression of StDFR and StANS as well as the accumulation of anthocyanins by enhancing the function of the MYB transcription factor StAN1. Furthermore, the interaction between StWRKY70 and StAN1 was verified by Y2H and BiFC. Our analysis discovered a new transcriptional activator StWRKY70 which potentially involved in tuber flesh pigmentation, thus may lay the foundation for deciphering how the WRKY-MYB-bHLH-WD40 (WRKY-MBW) complex regulate the accumulation of anthocyanins and provide new strategies to breed for more nutritious potato varieties with enhanced tuber flesh anthocyanins.

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.

Comparative transcriptomic analysis of the nodulation-competent zone and inference of transcription regulatory network in silicon applied Glycine max [L.]-Merr. Roots

KEY MESSAGE

The study unveils Si's regulatory influence by regulating DEGs, TFs, and TRs. Further bHLH subfamily and auxin transporter pathway elucidates the mechanisms enhancing root development and nodulation. Soybean is a globally important crop serving as a primary source of vegetable protein for millions of individuals. The roots of these plants harbour essential nitrogen fixing structures called nodules. This study investigates the multifaceted impact of silicon (Si) application on soybean, with a focus on root development, and nodulation employing comprehensive transcriptomic analyses and gene regulatory network. RNA sequence analysis was utilised to examine the change in gene expression and identify the noteworthy differentially expressed genes (DEGs) linked to the enhancement of soybean root nodulation and root development. A set of 316 genes involved in diverse biological and molecular pathways are identified, with emphasis on transcription factors (TFs) and transcriptional regulators (TRs). The study uncovers TF and TR genes, categorized into 68 distinct families, highlighting the intricate regulatory landscape influenced by Si in soybeans. Upregulated most important bHLH subfamily and the involvement of the auxin transporter pathway underscore the molecular mechanisms contributing to enhanced root development and nodulation. The study bridges insights from other research, reinforcing Si's impact on stress-response pathways and phenylpropanoid biosynthesis crucial for nodulation. The study reveals significant alterations in gene expression patterns associated with cellular component functions, root development, and nodulation in response to Si.

For a Colorful Life: Recent Advances in Anthocyanin Biosynthesis during Leaf Senescence

Leaf senescence is the last stage of leaf development, and it is accompanied by a leaf color change. In some species, anthocyanins are accumulated during leaf senescence, which are vital indicators for both ornamental and commercial value. Therefore, it is essential to understand the molecular mechanism of anthocyanin accumulation during leaf senescence, which would provide new insight into autumn coloration and molecular breeding for more colorful plants. Anthocyanin accumulation is a surprisingly complex process, and significant advances have been made in the past decades. In this review, we focused on leaf coloration during senescence. We emphatically discussed several networks linked to genetic, hormonal, environmental, and nutritional factors in regulating anthocyanin accumulation during leaf senescence. This paper aims to provide a regulatory model for leaf coloration and to put forward some prospects for future development.

Plant secondary metabolism in a fluctuating world: climate change perspectives

Climate changes have unpredictable effects on ecosystems and agriculture. Plants adapt metabolically to overcome these challenges, with plant secondary metabolites (PSMs) being crucial for plant-environment interactions. Thus, understanding how PSMs respond to climate change is vital for future cultivation and breeding strategies. Here, we review PSM responses to climate changes such as elevated carbon dioxide, ozone, nitrogen deposition, heat and drought, as well as a combinations of different factors. These responses are complex, depending on stress dosage and duration, and metabolite classes. We finally identify mechanisms by which climate change affects PSM production ecologically and molecularly. While these observations provide insights into PSM responses to climate changes and the underlying regulatory mechanisms, considerable further research is required for a comprehensive understanding.

CsMYB73 negatively regulates theanine accumulation mediated by CsGGT2 and CsGGT4 in tea shoots (Camellia sinensis)

Theanine metabolism is a necessary biological process during the planting and production of tea that determines tea quality. There is currently little knowledge about the transcriptional regulation of theanine metabolism in tea plants. In this study, we demonstrated that γ-glutamyl-transpeptidase CsGGT4, as a homologous protein of the theanine hydrolase CsGGT2, exhibited a higher theanine synthesis catalytic efficiency. Homology modeling and molecular docking showed that differential protein structures between CsGGT2 and CsGGT4 implied their different biological functions in tea plants. Theanine content correlated significantly with the expression of CsGGT2, CsGGT4 and the transcription factor CsMYB73 in tea shoots from different seasons. Additionally, CsMYB73 was confirmed to act as a nucleus-localized transcription factor (TF), directly interacts with the CsGGT2 and CsGGT4 promoters, serving as an activator of CsGGT2 and a suppressor of CsGGT4. Consequently, this leads to a negative association with theanine accumulation in tea shoots. Furthermore, the continuous increase in CsMYB73 produced a significantly increase in CsGGT2 expression and inhibited CsGGT4 expression. The present study reveals that the degradation of theanine has been observed to increase, concomitantly with the inhibition of theanine synthesis, resulting in a significant decline in the accumulation of theanine in tea shoots during the process of seasonal greening in 'Huangkui' leaves. This study contributes to the broader comprehension of the intricate transcriptional regulatory hierarchy that governs the metabolism of theanine in tea shoots, offering novel approaches for managing tea plantations and enhancing tea quality.

Molecular mechanism of miRNA mediated biosynthesis of secondary metabolites in medicinal plants

Plant secondary metabolites are important raw materials for the pharmaceutical industry, and their biosynthetic processes are subject to diverse and precise regulation by miRNA. The identification of miRNA molecules in medicinal plants and exploration of their mechanisms not only contribute to a deeper understanding of the molecular genetic mechanisms of plant growth, development and resistance to stress, but also provide a theoretical basis for elucidating the pharmacological effects of authentic medicinal materials and constructing bioreactors for the synthesis of medicinal secondary metabolite components. This paper summarizes the research reports on the discovery of miRNA in medicinal plants and their regulatory mechanisms on the synthesis of secondary metabolites by searching the relevant literature in public databases. It summarizes the currently discovered miRNA and their functions in medicinal plants, and summarizes the molecular mechanisms regulating the synthesis and degradation of secondary metabolites. Furthermore, it provides a prospect for the research and development of medicinal plant miRNA. The compiled information contributes to a comprehensive understanding of the research progress on miRNA in medicinal plants and provides a reference for the industrial development of related secondary metabolite biosynthesis.

Cloned genes and genetic regulation of anthocyanin biosynthesis in maize, a comparative review

Anthocyanins are plant-based pigments that are primarily present in berries, grapes, purple yam, purple corn and black rice. The research on fruit corn with a high anthocyanin content is not sufficiently extensive. Considering its crucial role in nutrition and health it is vital to conduct further studies on how anthocyanin accumulates in fruit corn and to explore its potential for edible and medicinal purposes. Anthocyanin biosynthesis plays an important role in maize stems (corn). Several beneficial compounds, particularly cyanidin-3-O-glucoside, perlagonidin-3-O-glucoside, peonidin 3-O-glucoside, and their malonylated derivatives have been identified. C1, C2, Pl1, Pl2, Sh2, ZmCOP1 and ZmHY5 harbored functional alleles that played a role in the biosynthesis of anthocyanins in maize. The Sh2 gene in maize regulates sugar-to-starch conversion, thereby influencing kernel quality and nutritional content. ZmCOP1 and ZmHY5 are key regulatory genes in maize that control light responses and photomorphogenesis. This review concludes the molecular identification of all the genes encoding structural enzymes of the anthocyanin pathway in maize by describing the cloning and characterization of these genes. Our study presents important new understandings of the molecular processes behind the manufacture of anthocyanins in maize, which will contribute to the development of genetically modified variants of the crop with increased color and possible health advantages.

The ncRNAs Involved in the Regulation of Abiotic Stress-Induced Anthocyanin Biosynthesis in Plants

Plants have evolved complicated defense and adaptive systems to grow in various abiotic stress environments such as drought, cold, and salinity. Anthocyanins belong to the secondary metabolites of flavonoids with strong antioxidant activity in response to various abiotic stress and enhance stress tolerance. Anthocyanin accumulation often accompanies the resistance to abiotic stress in plants to scavenge reactive oxygen species (ROS). Recent research evidence showed that many regulatory pathways such as osmoregulation, antioxidant response, plant hormone response, photosynthesis, and respiration regulation are involved in plant adaption to stress. However, the molecular regulatory mechanisms involved in controlling anthocyanin biosynthesis in relation to abiotic stress response have remained obscure. Here, we summarize the current research progress of specific regulators including small RNAs, and lncRNAs involved in the molecular regulation of abiotic stress-induced anthocyanin biosynthesis. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by microRNAs (miRNAs), long non-coding RNAs (lncRNAs), transcription factors, and stress response factors is also discussed. Understanding molecular mechanisms of anthocyanin biosynthesis for ROS scavenging in various abiotic stress responses will benefit us for resistance breeding in crop plants.

Distinct heat response molecular mechanisms emerge in cassava vasculature compared to leaf mesophyll tissue under high temperature stress

With growing concerns over global warming, cultivating heat-tolerant crops has become paramount to prepare for the anticipated warmer climate. Cassava (Manihot esculenta Crantz), a vital tropical crop, demonstrates exceptional growth and productivity under high-temperature (HT) conditions. Yet, studies elucidating HT resistance mechanisms in cassava, particularly within vascular tissues, are rare. We dissected the leaf mid-vein from leaf, and did the comparative transcriptome profiling between mid-vein and leaf to figure out the cassava vasculature HT resistance molecular mechanism. Anatomical microscopy revealed that cassava leaf veins predominantly consisted of vasculature. A thermal imaging analysis indicated that cassava experienced elevated temperatures, coinciding with a reduction in photosynthesis. Transcriptome sequencing produced clean reads in total of 89.17G. Using Venn enrichment, there were 65 differentially expressed genes (DEGs) and 93 DEGs had been found highly specifically expressed in leaf and mid-vein. Further investigation disclosed that leaves enhanced pyruvate synthesis as a strategy to withstand high temperatures, while mid-veins fortified themselves by bolstering lignin synthesis by comprehensive GO and KEGG analysis of DEGs. The identified genes in these metabolic pathways were corroborated through quantity PCR (QPCR), with results aligning with the transcriptomic data. To verify the expression localization of DEGs, we used in situ hybridization experiments to identify the expression of MeCCoAMT(caffeoyl-coenzyme A-3-O-methyltransferase) in the lignin synthesis pathway in cassava leaf veins xylem. These findings unravel the disparate thermotolerance mechanisms exhibited by cassava leaves and mid-veins, offering insights that could potentially inform strategies for enhancing thermotolerance in other crops.

Analysis of bZIP gene family in lotus (Nelumbo) and functional study of NnbZIP36 in regulating anthocyanin synthesis

BACKGROUND

The basic leucine zipper (bZIP) family is a predominant group of transcription factors in plants, involved in regulating plant growth, development, and response to stressors. Additionally, the bZIP gene family has a key role in anthocyanin production. Despite the significant role of bZIP genes in plants, their potential contribution in lotus remains understudied.

RESULTS

A total of 124 bZIP genes (59 NnbZIPs and 65 NlbZIPs) were identified from genomes of two lotus species. These genes were classified into 13 groups according to the grouping principle of the Arabidopsis bZIP gene family. Analysis of promoter cis-acting elements indicated that most bZIP gene family members in lotus are associated with response to abiotic stresses. The promoters of some bZIP genes contain MYB binding sites that regulate anthocyanin synthesis. We examined the anthocyanin content of the petals from three different colored lotus, combined with transcriptome data analysis and qRT-PCR results, showing that the expression trends of NnbZIP36 and the homologous gene NlbZIP38 were significantly correlated with the anthocyanin content in lotus petals. Furthermore, we found that overexpression of NnbZIP36 in Arabidopsis promoted anthocyanin accumulation by upregulating the expression of genes (4CL, CHI, CHS, F3H, F3'H, DFR, ANS and UF3GT) related to anthocyanin synthesis.

CONCLUSIONS

Our study enhances the understanding of the bZIP gene family in lotus and provides evidence for the role of NnbZIP36 in regulating anthocyanin synthesis. This study also sets the stage for future investigations into the mechanism by which the bZIP gene family regulates anthocyanin biosynthesis in lotus.

Artificial warming affects sugar signals and flavonoid accumulation to improve female willows' growth faster than males

Increasing global warming is severely affecting tree growth and development. However, research on the sex-specific responses of dioecious trees to warming is scarce. Here, male and female Salix paraplesia were selected for artificial warming (an increase of 4 °C relative to ambient temperature) to investigate the effects on morphological, physiological, biochemical and molecular responses. The results showed that warming significantly promoted the growth of female and male S. paraplesia, but females grew faster than males. Warming affected photosynthesis, chloroplast structures, peroxidase activity, proline, flavonoids, nonstructural carbohydrates (NSCs) and phenolic contents in both sexes. Interestingly, warming increased flavonoid accumulation in female roots and male leaves but inhibited it in female leaves and male roots. The transcriptome and proteome results indicated that differentially expressed genes and proteins were significantly enriched in sucrose and starch metabolism and flavonoid biosynthesis pathways. The integrative analysis of transcriptomic, proteomic, biochemical and physiological data revealed that warming changed the expression of SpAMY, SpBGL, SpEGLC and SpAGPase genes, resulting in the reduction of NSCs and starch and the activation of sugar signaling, particularly SpSnRK1s, in female roots and male leaves. These sugar signals subsequently altered the expression of SpHCTs, SpLAR and SpDFR in the flavonoid biosynthetic pathway, ultimately leading to the differential accumulation of flavonoids in female and male S. paraplesia. Therefore, warming causes sexually differential responses of S. paraplesia, with females performing better than males.

Integrated transcriptomic and metabolomic analysis revealed altitude-related regulatory mechanisms on flavonoid accumulation in potato tubers

Not least because it is adaptable to a variety of geographies and climates, potato (Solanum tuberosum L.) is grown across much of the world. Pigmented potato tubers have been found to contain large quantities of flavonoids, which have various functional roles and act as antioxidants in the human diet. However, the effect of altitude on the biosynthesis and accumulation of flavonoids in potato tubers is poorly characterized. Here we carried out an integrated metabolomic and transcriptomic study in order to evaluate how cultivation at low (800 m), moderate (1800 m), and high (3600 m) altitude affects flavonoid biosynthesis in pigmented potato tubers. Both red and purple potato tubers grown at a high altitude contained the highest flavonoid content, and the most highly pigmented flesh, followed by those grown at a low altitude. Co-expression network analysis revealed three modules containing genes which were positively correlated with altitude-responsive flavonoid accumulation. The anthocyanin repressors StMYBATV and StMYB3 exhibited a significant positive relationship with altitude-responsive flavonoid accumulation. The repressive function of StMYB3 was further verified in tobacco flowers and potato tubers. The results presented here add to the growing body of knowledge regarding the response of flavonoid biosynthesis to environmental conditions, and should aid in efforts to develop novel varieties of pigmented potatoes for use across different geographies.

Silicon Induces Heat and Salinity Tolerance in Wheat by Increasing Antioxidant Activities, Photosynthetic Activity, Nutrient Homeostasis, and Osmo-Protectant Synthesis

Modern agriculture is facing the challenges of salinity and heat stresses, which pose a serious threat to crop productivity and global food security. Thus, it is necessary to develop the appropriate measures to minimize the impacts of these serious stresses on field crops. Silicon (Si) is the second most abundant element on earth and has been recognized as an important substance to mitigate the adverse effects of abiotic stresses. Thus, the present study determined the role of Si in mitigating adverse impacts of salinity stress (SS) and heat stress (HS) on wheat crop. This study examined response of different wheat genotypes, namely Akbar-2019, Subhani-2021, and Faisalabad-2008, under different treatments: control, SS (8 dSm^-1), HS, SS + HS, control + Si, SS + Si, HS+ Si, and SS + HS+ Si. This study's findings reveal that HS and SS caused a significant decrease in the growth and yield of wheat by increasing electrolyte leakage (EL), malondialdehyde (MDA), and hydrogen peroxide (H₂O₂) production; sodium (Na⁺) and chloride (Cl^-) accumulation; and decreasing relative water content (RWC), chlorophyll and carotenoid content, total soluble proteins (TSP), and free amino acids (FAA), as well as nutrient uptake (potassium, K; calcium, Ca; and magnesium, Mg). However, Si application offsets the negative effects of both salinity and HS and improved the growth and yield of wheat by increasing chlorophyll and carotenoid contents, RWC, antioxidant activity, TSP, FAA accumulation, and nutrient uptake (Ca, K, and Mg); decreasing EL, electrolyte leakage, MDA, and H₂O₂; and restricting the uptake of Na⁺ and Cl^-. Thus, the application of Si could be an important approach to improve wheat growth and yield under normal and combined saline and HS conditions by improving plant physiological functioning, antioxidant activities, nutrient homeostasis, and osmolyte accumulation.

Persulfidation of transcription factor MYB10 inhibits anthocyanin synthesis in red-skinned pear

Hydrogen sulfide (H2S) is a gaseous signaling molecule that delays color change during fruit ripening. Whether H2S affects anthocyanin biosynthesis in red-skinned pears (Pyrus L.) remains unclear. Here, we found that H2S substantially inhibits anthocyanin accumulation in red-skinned pears and the expression of several genes encoding transcription factors is affected in response to H2S signaling. For example, PyMYB10 and PyMYB73 were down-regulated, whereas PyMYB114 and PyMYB6 were up-regulated. Bioinformatics analysis showed that PyMYB73 and PyMYB6, each containing an EAR motif, may negatively regulate anthocyanin accumulation. Transient expression analysis showed that PyMYB73 substantially promotes anthocyanin biosynthesis by co-transforming with PyMYB10/PyMYB114 + PybHLH3; however, PyMYB6 inhibited anthocyanin biosynthesis in strawberry (Fragaria vesca) receptacles and pear fruits, and PyMYB73 interacted with PyMYB10 and PyMYB6 but not PyMYB114 or PybHLH3. Further investigation showed that Cys194 and Cys218 of PyMYB10 were modified by persulfidation and that PyMYB10Cys218Ala substantially increased anthocyanin accumulation by a transient transformation system. Co-transformation of PyMYB10Cys218Ala + PyMYB73/PyMYB6 also promoted anthocyanin accumulation in pear fruits. Yeast two-hybrid assays showed that the mutation of PyMYB10 did not affect the interaction between PyMYB10 and PyMYB73, but it inhibited interaction with PyMYB6. Moreover, H2S weakened the interaction between PyMYB10 and PyMYB73 but enhanced the interaction with PyMYB6. Thus, we provided a model in which PyMYB10 undergoes persulfidation at Cys218, enhancing the interaction with PyMYB6 and reducing the interaction with PyMYB73. These subsequently results in lower expression of the anthocyanin biosynthesis-related genes Pyrus dihydroflavonol 4-reductase (PyDFR), Pyrus anthocyanidin synthase (PyANS), Pyrus UDP-glucose: flavonoid 3-glucosyl transferase (PyUFGT) and Pyrus glutathione S-transferase (PyGST), thereby inhibiting anthocyanin accumulation in red-skinned pears. Our findings provided a molecular mechanism for H2S-mediated anthocyanin biosynthesis in red-skinned pears.

The transcription factor CmERFI-2 represses CmMYB44 expression to increase sucrose levels in oriental melon fruit

Soluble sugar accumulation in fruit ripening determines fleshy fruit quality. However, the molecular mechanism for this process is not yet understood. Here, we showed a transcriptional repressor, CmMYB44 regulates sucrose accumulation and ethylene synthesis in oriental melon (Cucumis. melo var. makuwa Makino) fruit. Overexpressing CmMYB44 suppressed sucrose accumulation and ethylene production. Furthermore, CmMYB44 repressed the transcriptional activation of CmSPS1 (sucrose phosphate synthase 1) and CmACO1 (ACC oxidase 1), two key genes in sucrose and ethylene accumulation, respectively. During the later stages of fruit ripening, the repressive effect of CmMYB44 on CmSPS1 and CmACO1 could be released by overexpressing CmERFI-2 (ethylene response factor I-2) and exogenous ethylene in "HS" fruit (high sucrose accumulation fruit). CmERFI-2 acted upstream of CmMYB44 as a repressor by directly binding the CmMYB44 promoter region, indirectly stimulating the expression level of CmSPS1 and CmACO1. Taken together, we provided a molecular regulatory pathway mediated by CmMYB44, which determines the degree of sucrose and ethylene accumulation in oriental melon fruit and sheds light on transcriptional responses triggered by ethylene sensing that enable the process of fruit ripening.

A comparative analysis of small RNA sequencing data in tubers of purple potato and its red mutant reveals small RNA regulation in anthocyanin biosynthesis

Anthocyanins are a group of natural pigments acting as stress protectants induced by biotic/abiotic stress in plants. Although the metabolic pathway of anthocyanin has been studied in potato, the roles of miRNAs on the metabolic pathway remain unclear. In this study, a purple tetraploid potato of SD92 and its red mutant of SD140 were selected to explore the regulation mechanism of miRNA in anthocyanin biosynthesis. A comparative analysis of small RNAs between SD92 and SD140 revealed that there were 179 differentially expressed miRNAs, including 65 up- and 114 down-regulated miRNAs. Furthermore, 31 differentially expressed miRNAs were predicted to potentially regulate 305 target genes. KEGG pathway enrichment analysis for these target genes showed that plant hormone signal transduction pathway and plant-pathogen interaction pathway were significantly enriched. The correlation analysis of miRNA sequencing data and transcriptome data showed that there were 140 negative regulatory miRNA-mRNA pairs. The miRNAs included miR171 family, miR172 family, miR530b_4 and novel_mir170. The mRNAs encoded transcription factors, hormone response factors and protein kinases. All these results indicated that miRNAs might regulate anthocyanin biosynthesis through transcription factors, hormone response factors and protein kinase.

Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes

Sweet potatoes (Ipomoea batatas) are one of the important tuberous root crops cultivated worldwide, and thier storage roots are rich in antioxidants, such as anthocyanins. R2R3-MYB is a large gene family involved in various biological processes, including anthocyanin biosynthesis. However, few reports about the R2R3-MYB gene family of sweet potatoes have been released to date. In the present study, a total of 695 typical R2R3-MYB genes were identified in six Ipomoea species, including 131 R2R3-MYB genes in sweet potatoes. A maximum likelihood phylogenetic analysis divided these genes into 36 clades, referring to the classification of 126 R2R3-MYB proteins of Arabidopsis. Clade C25(S12) has no members in six Ipomoea species, whereas four clades (i.e., clade C21, C26, C30, and C36), including 102 members, had no members in Arabidopsis, and they were identified as Ipomoea-specific clades. The identified R2R3-MYB genes were unevenly distributed on all chromosomes in six Ipomoea species genomes, and the collinearity analysis among hexaploid I. batatas and another five diploid Ipomoea species suggested that the sweet potato genome might have undergone a larger chromosome rearrangement during the evolution process. Further analyses of gene duplication events showed that whole-genome duplication, transposed duplication, and dispersed duplication events were the primary forces driving the R2R3-MYB gene family expansion of Ipomoea plants, and these duplicated genes experienced strong purifying selection because of their Ka/Ks ratio, which is less than 1. Additionally, the genomic sequence length of 131 IbR2R3-MYBs varied from 923 bp to ~12.9 kb with a mean of ~2.6 kb, and most of them had more than three exons. The Motif 1, 2, 3, and 4 formed typical R2 and R3 domains and were identified in all IbR2R3-MYB proteins. Finally, based on multiple RNA-seq datasets, two IbR2R3-MYB genes (IbMYB1/g17138.t1 and IbMYB113/g17108.t1) were relatively highly expressed in pigmented leaves and tuberous root flesh and skin, respectively; thus, they were identified to regulate tissue-specific anthocyanin accumulation in sweet potato. This study provides a basis for the evolution and function of the R2R3-MYB gene family in sweet potatoes and five other Ipomoea species.

Comprehensive Analysis of bHLH Transcription Factors in Ipomoea aquatica and Its Response to Anthocyanin Biosynthesis

The basic helix-loop-helix (bHLH) proteins compose one of the largest transcription factor (TF) families in plants, which play a vital role in regulating plant biological processes including growth and development, stress response, and secondary metabolite biosynthesis. Ipomoea aquatica is one of the most important nutrient-rich vegetables. Compared to the common green-stemmed I. aquatica, purple-stemmed I. aquatica has extremely high contents of anthocyanins. However, the information on bHLH genes in I. aquatica and their role in regulating anthocyanin accumulation is still unclear. In this study, we confirmed a total of 157 bHLH genes in the I. aquatica genome, which were classified into 23 subgroups according to their phylogenetic relationship with the bHLH of Arabidopsis thaliana (AtbHLH). Of these, 129 IabHLH genes were unevenly distributed across 15 chromosomes, while 28 IabHLH genes were spread on the scaffolds. Subcellular localization prediction revealed that most IabHLH proteins were localized in the nucleus, while some were in the chloroplast, extracellular space, and endomembrane system. Sequence analysis revealed conserved motif distribution and similar patterns of gene structure within IabHLH genes of the same subfamily. Analysis of gene duplication events indicated that DSD and WGD played a vital role in the IabHLH gene family expansion. Transcriptome analysis showed that the expression levels of 13 IabHLH genes were significantly different between the two varieties. Of these, the IabHLH027 had the highest expression fold change, and its expression level was dramatically higher in purple-stemmed I. aquatica than that in green-stemmed I. aquatica. All upregulated DEGs in purple-stemmed I. aquatica exhibited the same expression trends in both qRT-PCR and RNA-seq. Three downregulated genes including IabHLH142, IabHLH057, and IabHLH043 determined by RNA-seq had opposite expression trends of those detected by qRT-PCR. Analysis of the cis-acting elements in the promoter region of 13 differentially expressed genes indicated that light-responsive elements were the most, followed by phytohormone-responsive elements and stress-responsive elements, while plant growth and development-responsive elements were the least. Taken together, this work provides valuable clues for further exploring IabHLH function and facilitating the breeding of anthocyanin-rich functional varieties of I. aquatica.

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.

Molecular mechanism of phosphorous signaling inducing anthocyanin accumulation in Arabidopsis

Anthocyanins, flavonoid compounds derived from secondary metabolic pathways, play important roles in various biological processes. Phosphorus (P) is an essential macroelement for plant growth and development, and P-starvation usually results in anthocyanin accumulation. However, the molecular mechanism of P deficiency promotes anthocyanin biosynthesis has not been well characterized. Here, we provided evidence that the P signaling core protein PHOSPHATE STARVATION RESPONSE1 (PHR1) is physically associate with transcription factors (TFs) involved in anthocyanidin biosynthesis, including PRODUCTION OF ANTHOCYANIN PIGMENTS1 (PAP1/MYB75), MYB DOMAIN PROTEIN 113 (MYB113) and TRANSPARENT TESTA 8 (TT8). PHR1 and its homologies positively regulated anthocyanin accumulation in Arabidopsis seedlings under P-deficient conditions. Disruption of PHR1 simultaneously rendered seedlings hyposensitive to limiting P, whereas the overexpression of PHR1 enhanced P- deficiency-induced anthocyanin accumulation. Genetic analysis demonstrated that 35S:PHR1-2HA-5 seedlings partially recovers the P deficiency insensitive phenotype of myb-RNAi and tt8 mutants. In summary, our study indicated that protein complexes formed by PHR1 and MBW complex directly mediate the process of P-deficiency-induced anthocyanin accumulation, providing a new mechanistic understanding of how P-deficient signaling depends on the endogenous anthocyanin synthesis pathway to promote anthocyanin accumulation in Arabidopsis.

Anthocyanins in Plant Food: Current Status, Genetic Modification, and Future Perspectives

Anthocyanins are naturally occurring polyphenolic pigments that give food varied colors. Because of their high antioxidant activities, the consumption of anthocyanins has been associated with the benefit of preventing various chronic diseases. However, due to natural evolution or human selection, anthocyanins are found only in certain species. Additionally, the insufficient levels of anthocyanins in the most common foods also limit the optimal benefits. To solve this problem, considerable work has been done on germplasm improvement of common species using novel gene editing or transgenic techniques. This review summarized the recent advances in the molecular mechanism of anthocyanin biosynthesis and focused on the progress in using the CRISPR/Cas gene editing or multigene overexpression methods to improve plant food anthocyanins content. In response to the concerns of genome modified food, the future trends in developing anthocyanin-enriched plant food by using novel transgene or marker-free genome modified technologies are discussed. We hope to provide new insights and ideas for better using natural products like anthocyanins to promote human health.

Efficacy of endophytic SB10 and glycine betaine duo in alleviating phytotoxic impact of combined heat and salinity in Glycine max L. via regulation of redox homeostasis and physiological and molecular responses

Adverse environmental stresses occurring simultaneously exhibit a lethal effect on crop productivity at the global level. Here, we investigated the individual and synergistic effects of endophytic T. virens SB10 and glycine betaine (GB) on the physiological and biochemical responses of Glycine max L. to alleviate the devastating effects of combined heat and salinity (HS) stress. Screening against HS stress tolerance showed that SB10 has significant tolerance against heat stress and produces hormones such as gibberellins and indole-3-acetic acid upon GB amendment of the growth medium under HS stress. Moreover, the current findings illustrated that the synergistic application of SB10 and GB was effective in alleviating the negative effects of HS stress on plant growth and physiology. The findings revealed that SB10 + GB led to a reduction in proline accumulation and Na⁺ uptake. It also maintained a high K⁺/Na ⁺ ratio by regulating GmHKT1 and GmSOS1 expression and enhanced macronutrient uptake (N, Ca, K) in plants. In turn, plants exhibited a higher growth rate and gaseous exchange attributes coupled with the upregulation of APX, SOD, POD, and GSH antioxidant activities and transcript accumulation of GmSOD1 and GmAPX1 to overcome HS-induced oxidative damage. Furthermore, SB10 + GB downregulated DREB2, DREB1B, and GmNCED3 expression and resulted in the reduced accumulation of endogenous ABA while enhancing endogenous SA accumulation via upregulation of PAL genes. In addition, enhanced accumulation of bioactive gibberellins (GA1, GA3, GA4, and GA7) was detected under HS stress in the SB10 + GB treatment group. Moreover, SB10 + GB also significantly regulated GmHsp90A2 and GmHsfA2 expression in tolerance against HS stress. The combination of SB10 and GB was shown to be an effective and alternative approach for growing G. max at high temperature coupled with saline conditions for sustainable agriculture.

Investigating the induction of polyphenol biosynthesis in the cultured Cycolocarya paliurus cells and the stimulatory mechanism of co-induction with 5-aminolevulinic acid and salicylic acid

Background: Plant cell culture technology is a potential way to produce polyphenols, however, this way is still trapped in the dilemma of low content and yield. Elicitation is regarded as one of the most effective ways to improve the output of the secondary metabolites, and therefore has attracted extensive attention. Methods: Five elicitors including 5-aminolevulinic acid (5-ALA), salicylic acid (SA), methyl jasmonate (MeJA), sodium nitroprusside (SNP) and Rhizopus Oryzae Elicitor (ROE) were used to improve the content and yield of polyphenols in the cultured Cyclocarya paliurus (C. paliurus) cells, and a co-induction technology of 5-ALA and SA was developed as a result. Meanwhile, the integrated analysis of transcriptome and metabolome was adopted to interpret the stimulation mechanism of co-induction with 5-ALA and SA. Results: Under the co-induction of 50 μM 5-ALA and SA, the content and yield of total polyphenols of the cultured cells reached 8.0 mg/g and 147.12 mg/L, respectively. The yields of cyanidin-3-O-galactoside, procyanidin B1 and catechin reached 28.83, 4.33 and 2.88 times that of the control group, respectively. It was found that expressions of TFs such as CpERF105, CpMYB10 and CpWRKY28 increased significantly, while CpMYB44 and CpTGA2 decreased. These great changes might further make the expression of CpF3'H (flavonoid 3'-monooxygenase), CpFLS (flavonol synthase), CpLAR (leucoanthocyanidin reductase), CpANS (anthocyanidin synthase) and Cp4CL (4-coumarate coenzyme A ligase) increase while CpANR (anthocyanidin reductase) and CpF3'5'H (flavonoid 3', 5'-hydroxylase) reduce, ultimately enhancing the polyphenols accumulation Conclusion: The co-induction of 5-ALA and SA can significantly promote polyphenol biosynthesis in the cultured C. paliurus cells by regulating the expression of key transcription factors and structural genes associated with polyphenol synthesis, and thus has a promising application.

Integrative analysis of metabolome and transcriptome reveals a dynamic regulatory network of potato tuber pigmentation

Potatoes consist of flavonoids that provide health benefits for human consumers. To learn more about how potato tuber flavonoid accumulation and flesh pigmentation are controlled, we analyzed the transcriptomic and metabolomic profile of potato tubers from three colored potato clones at three developmental phases using an integrated approach. From the 72 flavonoids identified in pigmented flesh, differential abundance was noted for anthocyanins, flavonols, and flavones. Weighted gene co-expression network analysis further allowed modules and candidate genes that positively or negatively regulate flavonoid biosynthesis to be identified. Furthermore, an R2R3-MYB repressor StMYB3 and an R3-MYB repressor StMYBATV involved in the modulation of anthocyanin biosynthesis during tuber development were identified. Both StMYB3 and StMYBATV could interact with the cofactor StbHLH1 and repress anthocyanin biosynthesis. Our results indicate a feedback regulatory mechanism of a coordinated MYB activator-repressor network on fine-tuning of potato tuber pigmentation during tuber development.

MYB44-ENAP1/2 restricts HDT4 to regulate drought tolerance in Arabidopsis

Histone acetylation has been shown to involve in stress responses. However, the detailed molecular mechanisms that how histone deacetylases and transcription factors function in drought stress response remain to be understood. In this research, we show that ENAP1 and ENAP2 are positive regulators of drought tolerance in plants, and the enap1enap2 double mutant is more sensitive to drought stress. Both ENAP1 and ENAP2 interact with MYB44, a transcription factor that interacts with histone deacetylase HDT4. Genetics data show that myb44 null mutation enhances the sensitivity of enap1enap2 to drought stress. Whereas, HDT4 negatively regulates plant drought response, the hdt4 mutant represses enap1enap2myb44 drought sensitive phenotype. In the normal condition, ENAP1/2 and MYB44 counteract the HDT4 function for the regulation of H3K27ac. Upon drought stress, the accumulation of MYB44 and reduction of HDT4 leads to the enrichment of H3K27ac and the activation of target gene expression. Overall, this research provides a novel molecular mechanism by which ENAP1, ENAP2 and MYB44 form a complex to restrict the function of HDT4 in the normal condition; under drought condition, accumulated MYB44 and reduced HDT4 lead to the elevation of H3K27ac and the expression of drought responsive genes, as a result, plants are drought tolerant.

Methylation level of potato gene OMT30376 regulates tuber anthocyanin transformations

After anthocyanin synthesis, a variety of anthocyanin compounds are produced through further methylation, glycosylation, and acylation. However, the effect of the potato methylase gene on anthocyanin biosynthesis has not been reported. Red and purple mutation types appear in tubers of the potato cultivar 'Purple Viking' with chimeric skin phenotypes. In this study, transcriptome and anthocyanin metabolome analyses were performed on skin of Purple Viking tubers and associated mutants. According to the metabolome analysis, the transformation of delphinidin into malvidin-3-O-glucoside and petunidin 3-O-glucoside and that of cyanidin into rosinidin O-hexoside and peonidin-3-O-glucoside were hindered in red tubers. Expression of methyltransferase gene OMT30376 was significantly lower in red tubers than in purple ones, whereas the methylation level of OMT30376 was significantly higher in red tubers. In addition, red skin appeared in tubers from purple tuber plants treated with S-adenosylmethionine (SAM), indicating the difference between purple and red was caused by the methylation degree of the gene OMT30376. Thus, the results of the study suggest that the OMT30376 gene is involved in the transformation of anthocyanins in potato tubers. The results also provide an important reference to reveal the regulatory mechanisms of anthocyanin biosynthesis and transformation.

Anthocyanin Biosynthesis Induced by MYB Transcription Factors in Plants

Anthocyanins act as polyphenolic pigment that is ubiquitously found in plants. Anthocyanins play a role not only in health-promoting as an antioxidant, but also in protection against all kinds of abiotic and biotic stresses. Most recent studies have found that MYB transcription factors (MYB TFs) could positively or negatively regulate anthocyanin biosynthesis. Understanding the roles of MYB TFs is essential in elucidating how MYB TFs regulate the accumulation of anthocyanin. In the review, we summarized the signaling pathways medicated by MYB TFs during anthocyanin biosynthesis including jasmonic acid (JA) signaling pathway, cytokinins (CKs) signaling pathway, temperature-induced, light signal, 26S proteasome pathway, NAC TFs, and bHLH TFs. Moreover, structural and regulator genes induced by MYB TFs, target genes bound and activated or suppressed by MYB TFs, and crosstalk between MYB TFs and other proteins, were found to be vitally important in the regulation of anthocyanin biosynthesis. In this study, we focus on the recent knowledge concerning the regulator signaling and mechanism of MYB TFs on anthocyanin biosynthesis, covering the signaling pathway, genes expression, and target genes and protein expression.

High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content

Highbush blueberry (Vaccinium corymbosum, 2n = 4x = 48) is the most cultivated type of blueberry, both in New Zealand and overseas. Its perceived nutritional value is conferred by phytonutrients, particularly anthocyanins. Identifying the genetic mechanisms that control the biosynthesis of these metabolites would enable faster development of cultivars with improved fruit qualities. Here, we used recently released tools for genetic mapping in autotetraploids to build a high-density linkage map in highbush blueberry and to detect quantitative trait loci (QTLs) for fruit anthocyanin content. Genotyping was performed by target sequencing, with ∼18,000 single nucleotide polymorphism (SNP) markers being mapped into 12 phased linkage groups (LGs). Fruits were harvested when ripe for two seasons and analyzed with high-performance liquid chromatography-mass spectrometry (HPLC-MS): 25 different anthocyanin compounds were identified and quantified. Two major QTLs that were stable across years were discovered, one on LG2 and one on LG4, and the underlying candidate genes were identified. Interestingly, the presence of anthocyanins containing acylated sugars appeared to be under strong genetic control. Information gained in this study will enable the design of molecular markers for marker-assisted selection and will help build a better understanding of the genetic control of anthocyanin biosynthesis in this crop.

Uncovering anthocyanin diversity in potato landraces (Solanum tuberosum L. Phureja) using RNA-seq

Potato (Solanum tuberosum L.) is the third largest source of antioxidants in the human diet, after maize and tomato. Potato landraces have particularly diverse contents of antioxidant compounds such as anthocyanins. We used this diversity to study the evolutionary and genetic basis of anthocyanin pigmentation. Specifically, we analyzed the transcriptomes and anthocyanin content of tubers from 37 landraces with different colorations. We conducted analyses of differential expression between potatoes with different colorations and used weighted correlation network analysis to identify genes whose expression is correlated to anthocyanin content across landraces. A very significant fraction of the genes identified in these two analyses had annotations related to the flavonoid-anthocyanin biosynthetic pathway, including 18 enzymes and 5 transcription factors. Importantly, the causal genes at the D, P and R loci governing anthocyanin accumulation in potato cultivars also showed correlations to anthocyanin production in the landraces studied here. Furthermore, we found that 60% of the genes identified in our study were located within anthocyanin QTLs. Finally, we identified new candidate enzymes and transcription factors that could have driven the diversification of anthocyanins. Our results indicate that many anthocyanins biosynthetic genes were manipulated in ancestral potato breeding and can be used in future breeding programs.

Integrating Transcriptomic and Metabolomic Analyses to Explore the Effect of Color Under Fruit Calyx on That of Fruit Apex in Eggplant (Solanum melongena L.)

Fruit color is an important commercial characteristic of eggplant (Solanum melongena L.), which affects both the profits of growers and consumer choice. Two eggplant inbred lines were discovered: “Z,” which is a light purple color under the fruit calyx, with purple on the fruit apex; and “L,” fruits of which are green under the calyx and at the apex. To determine the molecular mechanisms underlying the effect of fruit peel color under the calyx on that at the fruit apex, we conducted a combined transcriptomic and metabolomic analyses of the Z and L inbred eggplant lines. Transcriptome analysis of peel samples from three fruit regions (under the calyx, the apex, and the middle surface) of each line was conducted by RNA sequencing, and generated a total of 791,512,404 clean reads from 18 samples (three biological replicates). Differentially expressed genes (DEGs; n = 424) were identified in comparisons of peel samples from the three sites of L line fruits. Gene ontology analysis showed that “catalytic activity” was extremely significantly enriched. Further, DEGs (n = 8) were enriched in the Kyoto Encyclopedia of Genes and Genomes pathway “flavonoid biosynthesis.” Levels of CHI, LDOX, F3′5′H, and dihydroflavonol reductase were higher in the Z line than the L line. In addition, metabolome analysis showed that, 10 differentially accumulated metabolites were detected between peel samples from the apex of L and Z line fruit. The most significant DAM was delphinidin-3-O-rutinoside (Z line content, 34.89 μg/g vs. L line content 0.01 μg/g). Combined transcriptomic and metabolomic analyses indicated that DFR and F3′5′H were closely related to content of the metabolites, cyanidin and delphinidin, and that some downstream metabolites differed significantly between the L and Z lines. Content levels of delphinidin-3-O-rutinoside, delphinidin-3-O-glucoside, cyanidin-3-O-glucoside, and cyanidin-3-O-rutinoside were markedly down-regulated in the L line. Altogether, increased CHI levels could up-regulate the downstream genes, LDOX, F3′5′H, and DFR, which further lead to increasing the content of delphindin. Thus, the uniform purple color was presented at the apex of fruits in Z plants. These findings not only identify key candidate genes, but will also improve understanding of the genetics and the efficiency of breeding for eggplant fruit color.

Temperature regulation of carotenoid accumulation in the petals of sweet osmanthus via modulating expression of carotenoid biosynthesis and degradation genes

Background

Temperature is involved in the regulation of carotenoid accumulation in many plants. The floral color of sweet osmanthus (Osmanthus fragrans Lour.) which is mainly contributed by carotenoid content, is affected by temperature in autumn. However, the mechanism remains unknown. Here, to reveal how temperature regulates the floral color of sweet osmanthus, potted sweet osmanthus ‘Jinqiu Gui’ were treated by different temperatures (15 °C, 19 °C or 32 °C). The floral color, carotenoid content, and the expression level of carotenoid-related genes in petals of sweet osmanthus ‘Jinqiu Gui’ under different temperature treatments were investigated.

Results

Compared to the control (19 °C), high temperature (32 °C) changed the floral color from yellow to yellowish-white with higher lightness (L*) value and lower redness (a*) value, while low temperature (15 °C) turned the floral color from yellow to pale orange with decreased L* value and increased a* value. Total carotenoid content and the content of individual carotenoids (α-carotene, β-carotene, α-cryptoxanthin, β-cryptoxanthin, lutein and zeaxanthin) were inhibited by high temperature, but were enhanced by low temperature. Lower carotenoid accumulation under high temperature was probably attributed to transcriptional down-regulation of the biosynthesis gene OfPSY1, OfZ-ISO1 and OfLCYB1, and up-regulation of degradation genes OfNCED3, OfCCD1-1, OfCCD1-2, and OfCCD4-1. Up-regulation of OfLCYB1, and down-regulation of OfNCED3 and OfCCD4-1 were predicted to be involved in low-temperature-regulated carotenoid accumulation. Luciferase assays showed that the promoter activity of OfLCYB1 was activated by low temperature, and repressed by high temperature. However, the promoter activity of OfCCD4-1 was repressed by low temperature, and activated by high temperature.

Conclusions

Our study revealed that high temperature suppressed the floral coloration by repressing the expression of carotenoid biosynthesis genes, and activating the expression of carotenoid degradation genes. However, the relative low temperature had opposite effects on floral coloration and carotenoid biosynthesis in sweet osmanthus. These results will help reveal the regulatory mechanism of temperature on carotenoid accumulation in the petals of sweet osmanthus.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08643-0.

Regulation of BcMYB44 on Anthocyanin Synthesis and Drought Tolerance in Non-Heading Chinese Cabbage (Brassica campestris ssp. chinensis Makino)

The purpose of this study was to explore the regulation of BcMYB44 on anthocyanin synthesis and drought tolerance of non-heading Chinese cabbage. The BcMYB44 gene was cloned from the purple inbred line ‘NJZX1-3’ and its green mutant ‘NJZX1-0’. Sequence analysis confirmed that BcMYB44 belongs to the R2R3-MYB family and has the highest homology with BnMYB44. Subcellular localization revealed that BcMYB44 is a nuclear protein. Yeast two-hybrid (Y2H) and Bimolecular Fluorescent Complimentary (BiFC) experiments showed that BcMYB44 interacts with BcPAP1 and BcEGL3. Pigment detection of BcPAP1 and BcMYB44 protein activity in N. benthamiana indicates that BcMYB44 plays a negative regulatory role by inhibiting the expression of key structural genes (F3H, DFR, etc.) in anthocyanin synthesis. Virus-induced gene silencing (VIGS) further confirmed this inhibition. Analysis of drought tolerance of non-heading Chinese cabbage based on VIGS showed that pTY-S plants are more resistant to drought than pTY-BcMYB44 plants. The results indicate that BcMYB44 has a positive regulatory role in drought stress, which most likely is achieved by inhibiting anthocyanin accumulation, regulating stomatal movement, and improving osmotic regulation and homeostasis of reactive oxygen species (ROS).

Transcriptome Analysis of Apples in High-Temperature Treatments Reveals a Role of MdLBD37 in the Inhibition of Anthocyanin Accumulation

Coloring in apple fruit due to anthocyanin accumulation is inhibited by high temperature; however, the underlying mechanism remains unclear. In the present study, total anthocyanin and cyanidin 3-galactoside contents were determined and compared between cv. ‘Redchief Delicious’ apple fruits at 25 °C and 35 °C treatments. The high temperature (35 °C) treatment substantially decreased total anthocyanin and cyanidin 3-galactoside contents. The transcriptomes of 25 °C- and 35 °C-treated apples were analyzed by high-throughput RNA sequencing. A total of 8354 differentially expressed genes (DEGs) were detected at four time points corresponding to the two temperature treatments. The up-regulated DEGs were annotated using GO as well as KEGG databases. A network module of 528 genes (including 21 transcription factors) most associated with the total anthocyanin and cyanidin 3-galactoside contents was constructed by weighted correlation network analysis (WGCNA). In the WGCNA module, we unearthed a LOB domain-containing gene designated as MdLBD37. The expression of MdLBD37 was sharply up-regulated by high temperature and negatively correlated with the total anthocyanin and cyanidin 3-galactoside contents. Overexpression of MdLBD37 in apple fruit and calli decreased the expression of anthocyanin biosynthetic genes, such as MdCHI, MdCHS, MdF3H, MdANS, MdDFR, and MdUFGT, along with anthocyanin accumulation. Our results suggested that MdLBD37 significantly influenced the high-temperature inhibition of anthocyanin accumulation in apples. The findings shed more light on the mechanism of anthocyanin inhibition during high-temperature stress in apples.

Evolution and functional diversification of R2R3-MYB transcription factors in plants

R2R3-MYB genes (R2R3-MYBs) form one of the largest transcription factor gene families in the plant kingdom, with substantial structural and functional diversity. However, the evolutionary processes leading to this amazing functional diversity have not yet been clearly established. Recently developed genomic and classical molecular technologies have provided detailed insights into the evolutionary relationships and functions of plant R2R3-MYBs. Here, we review recent genome-level and functional analyses of plant R2R3-MYBs, with an emphasis on their evolution and functional diversification. In land plants, this gene family underwent a large expansion by whole genome duplications and small-scale duplications. Along with this population explosion, a series of functionally conserved or lineage-specific subfamilies/groups arose with roles in three major plant-specific biological processes: development and cell differentiation, specialized metabolism, and biotic and abiotic stresses. The rapid expansion and functional diversification of plant R2R3-MYBs are highly consistent with the increasing complexity of angiosperms. In particular, recently derived R2R3-MYBs with three highly homologous intron patterns (a, b, and c) are disproportionately related to specialized metabolism and have become the predominant subfamilies in land plant genomes. The evolution of plant R2R3-MYBs is an active area of research, and further studies are expected to improve our understanding of the evolution and functional diversification of this gene family.

Ethylene precisely regulates anthocyanin synthesis in apple via a module comprising MdEIL1, MdMYB1, and MdMYB17

Ethylene regulates anthocyanin synthesis in ripening apple fruit via the antagonistic activities of the R2R3-MYB repressors and activators. However, the molecular mechanism underlying this process remains unknown. In this study, ethylene significantly induced the expression of the R2R3-MYB gene MdMYB17 in apple fruit. Moreover, MdMYB17 was revealed to be an important repressor of anthocyanin synthesis. Specifically, MdMYB17 binds directly to the promoters of the ethylene-induced genes MdMYB1 and MdEIL1, which encode positive regulators of anthocyanin synthesis, and represses their expression. Additionally, MdMYB1 and MdEIL1 bind to the MdMYB17 promoter to activate its expression. Thus, MdMYB17, MdMYB1, and MdEIL1 form a regulatory module that controls the expression of the corresponding genes. MdMYB17 interacts with MdEIL1. The interaction between MdMYB17 and MdEIL1 attenuates the regulatory effects of MdMYB17 on MdMYB1 and MdEIL1 as well as the regulatory effects of MdEIL1 on MdMYB17. Overall, our results reveal the molecular mechanisms by which MdMYB17, MdMYB1, and MdEIL1 finely mediate ethylene-regulated anthocyanin synthesis in apple fruit.

Impact of Single and Combined Salinity and High-Temperature Stresses on Agro-Physiological, Biochemical, and Transcriptional Responses in Rice and Stress-Release

Here, for the first time, we aimed to identify in rice the key mechanisms and processes underlying tolerance to high-temperature (HT) or salt stress (SS) alone, the co-occurrence of both stresses, and recovery using physiological and biochemical measurements and gene expression analysis. We also investigated whether recovery from the two stressors depended on the relative intensities/relief of each stressor. Wild type ('Yukinkomai') rice plants were found to be more susceptible to salinity or heat applied individually. SS leads to a depletion of cellular water content, higher accumulation of Na⁺, and alterations in photosynthetic pigments. The stress-tolerant cultivar 'YNU31-2-4' (YNU) displayed a lower Na⁺/K⁺ ratio, higher water content in cells and improved photosynthetic traits, antioxidant system, and expression of defence genes. Strikingly, the SS + HT combination provided a significant level of protection to rice plants from the effects of SS alone. The expression pattern of a selected set of genes showed a specific response and dedicated pathways in plants subjected to each of the different stresses, while other genes were explicitly activated when the stresses were combined. Aquaporin genes were activated by SS, while stress-related (P5CS, MSD1, HSPs, and ions transporters) genes were shaped by HT. Hierarchical clustering and principal component analyses showed that several traits exhibited a gradually aggravating effect as plants were exposed to the combined stresses and identified heat as a mitigating factor, clearly separating heat + salt-stressed from salt-non-heat-stressed plants. Furthermore, seedling recovery was far more dependent on the relative intensities of stressors and cultivars, demonstrating the influence of one stressor over another upon stress-release. Taken together, our data show the uniqueness and complexity of the physiological and molecular network modules used by rice plants to respond to single and combined stresses and recovery.

A Survey of Enhanced Cold Tolerance and Low-Temperature-Induced Anthocyanin Accumulation in a Novel Zoysia japonica Biotype

Zoysia japonica is a warm-season turfgrass that is extensively used in landscaping, sports fields, and golf courses worldwide. Uncovering the low-temperature response mechanism of Z. japonica can help to accelerate the development of new cold-tolerant cultivars, which could be used to prolong the ornamental and usage duration of turf. A novel Z. japonica biotype, YueNong-9 (YN-9), was collected from northeastern China for this study. Phenotypic measurements, cold-tolerance investigation, and whole-transcriptome surveys were performed on YN-9 and LanYin-3 (LY-3), the most popular Z. japonica cultivar in Southern China. The results indicated the following: YN-9 has longer second and third leaves than LY-3; when exposed to the natural low temperature during winter in Guangzhou, YN-9 accumulated 4.74 times more anthocyanin than LY-3; after cold acclimation and freezing treatment, 83.25 ± 9.55% of YN-9 survived while all LY-3 leaves died, and the dark green color index (DGCI) value of YN-9 was 1.78 times that of LY-3; in YN-9, there was a unique up-regulation of Phenylalanine ammonia-lyase (PAL), Homeobox-leucine Zipper IV (HD-ZIP), and ATP-Binding Cassette transporter B8 (ABCB8) expressions, as well as a unique down-regulation of zinc-regulated transporters and iron-regulated transporter-like proteins (ZIPs) expression, which may promote anthocyanin biosynthesis, transport, and accumulation. In conclusion, YN-9 exhibited enhanced cold tolerance and is thus an excellent candidate for breeding cold-tolerant Z. japonica variety, and its unique low-temperature-induced anthocyanin accumulation and gene responses provide ideas and candidate genes for the study of low-temperature tolerance mechanisms and genetic engineering breeding.

MrMYB44-Like Negatively Regulates Anthocyanin Biosynthesis and Causes Spring Leaf Color of Malus 'Radiant' to Fade From Red to Green

The "Spring-red-leaf" crabapple cultivar has young red leaves and mature green leaves. However, the mechanism of anthocyanin biosynthesis in crabapple leaves in spring remains unknown. In this study, Illumina RNA sequencing (RNA-Seq) was performed on Malus 'Radiant' leaf tissues in different stages of development. Twenty-two genes in the anthocyanin biosynthesis pathway and 44 MYB transcription factors (TFs) were significantly enriched among differentially expressed genes (DEGs). Three R2R3-MYB TFs in subgroup 22 of the MYB TF family, MrMYB44-like1, MrMYB44-like2, and MrMYB44-like3, were highly expressed in green leaves according to RNA-Seq and quantitative real-time quantitative PCR results. Their expression levels were negatively correlated with anthocyanin content. In transient assays, overexpression of MrMYB44-like1, MrMYB44-like2, or MrMYB44-like3 inhibited anthocyanin accumulation and reduced pigment in leaf disks of M. 'Radiant' and fruit peels of M. domestica 'Fuji.' When the conserved region of the three MrMYB44-likes was silenced, the anthocyanin biosynthesis pathway was activated and pigments increased in both tissues. Moreover, bimolecular fluorescence complementation assays showed MrMYB44-likes interacted with MrWRKY6 to form protein complexes that regulated anthocyanin biosynthesis.

Multilevel regulation of anthocyanin-promoting R2R3-MYB transcription factors in plants

Anthocyanins are common secondary metabolites in plants that confer red, blue, and purple colorations in plants and are highly desired by consumers for their visual appearance and nutritional quality. In the last two decades, the anthocyanin biosynthetic pathway and transcriptional regulation of anthocyanin biosynthetic genes (ABGs) have been well characterized in many plants. From numerous studies on model plants and horticultural crops, many signaling regulators have been found to control anthocyanin accumulation via regulation of anthocyanin-promoting R2R3-MYB transcription factors (so-called R2R3-MYB activators). The regulatory mechanism of R2R3-MYB activators is mediated by multiple environmental factors (e.g., light, temperature) and internal signals (e.g., sugar, ethylene, and JA) in complicated interactions at multiple levels. Here, we summarize the transcriptional control of R2R3-MYB activators as a result of natural variations in the promoter of their encoding genes, upstream transcription factors and epigenetics, and posttranslational modifications of R2R3-MYB that determine color variations of horticultural plants. In addition, we focus on progress in elucidating the integrated regulatory network of anthocyanin biosynthesis mediated by R2R3-MYB activators in response to multiple signals. We also highlight a few gene cascade modules involved in the regulation of anthocyanin-related R2R3-MYB to provide insights into anthocyanin production in horticultural plants.

Comparative Transcriptome Analysis Identifies Key Regulatory Genes Involved in Anthocyanin Metabolism During Flower Development in Lycoris radiata

Lycoris is used as a garden flower due to the colorful and its special flowers. Floral coloration of Lycoris is a vital trait that is mainly regulated via the anthocyanin biosynthetic pathway. In this study, we performed a comparative transcriptome analysis of Lycoris radiata petals at four different flower development stages. A total of 38,798 differentially expressed genes (DEGs) were identified by RNA sequencing, and the correlation between the expression level of the DEGs and the anthocyanin content was explored. The identified DEGs are significantly categorized into 'flavonoid biosynthesis,' 'phenylpropanoid biosynthesis,' 'Tropane, piperidine and pyridine alkaloid biosynthesis,' 'terpenoid backbone biosynthesis' and 'plant hormone signal transduction' by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The candidate genes involved in anthocyanin accumulation in L. radiata petals during flower development stages were also identified, which included 56 structural genes (especially LrDFR1 and LrFLS) as well as 27 key transcription factor DEGs (such as C3H, GATA, MYB, and NAC). In addition, a key structural gene namely LrDFR1 of anthocyanin biosynthesis pathway was identified as a hub gene in anthocyanin metabolism network. During flower development stages, the expression level of LrDFR1 was positively correlated with the anthocyanin content. Subcellular localization revealed that LrDFR1 is majorly localized in the nucleus, cytoplasm and cell membrane. Overexpression of LrDFR1 increased the anthocyanin accumulation in tobacco leaves and Lycoris petals, suggesting that LrDFR1 acts as a positively regulator of anthocyanin biosynthesis. Our results provide new insights for elucidating the function of anthocyanins in L. radiata petal coloring during flower development.

A light-responsive transcription factor SmMYB35 enhances anthocyanin biosynthesis in eggplant (Solanum melongena L.)

SmMYB35, a light-responsive R2R3-MYB transcription factor, positively regulates anthocyanin biosynthesis in eggplant by binding to the promoters of SmCHS, SmF3H, SmDFR, and SmANS and enhancing their activities. In addition, SmMYB35 interacts with SmTT8 and SmTTG1 to form a MBW complex, thereby enhancing anthocyanin biosynthesis. Eggplant is a vegetable rich in anthocyanins. SmMYB35, a light-responsive R2R3-MYB transcription factor, was isolated from eggplant and investigated for its biological functions. The results suggested that the expression of SmMYB35 was regulated by SmHY5 through directly binding to G-box in the promoter region, and the overexpression of SmMYB35 could increase the anthocyanin content in the stems and petals of the transgenic eggplants. SmMYB35 could also bind to the promoters of SmCHS, SmF3H, SmDFR, and SmANS and enhance their activities. In addition, SmMYB35 interacted with SmTT8 and SmTTG1 to form a MBW complex which enhanced anthocyanin biosynthesis. Taking together, we firstly verified that SmMYB35 promoted anthocyanin biosynthesis in plants. The results provide new insights into the regulatory effects of SmMYB35 on key anthocyanin biosynthetic genes and advance our understanding of the molecular mechanism of light-induced anthocyanin synthesis in eggplants.

A light-responsive transcription factor SmMYB35 enhances anthocyanin biosynthesis in eggplant (Solanum melongena L.)

SmMYB35, a light-responsive R2R3-MYB transcription factor, positively regulates anthocyanin biosynthesis in eggplant by binding to the promoters of SmCHS, SmF3H, SmDFR, and SmANS and enhancing their activities. In addition, SmMYB35 interacts with SmTT8 and SmTTG1 to form a MBW complex, thereby enhancing anthocyanin biosynthesis. Eggplant is a vegetable rich in anthocyanins. SmMYB35, a light-responsive R2R3-MYB transcription factor, was isolated from eggplant and investigated for its biological functions. The results suggested that the expression of SmMYB35 was regulated by SmHY5 through directly binding to G-box in the promoter region, and the overexpression of SmMYB35 could increase the anthocyanin content in the stems and petals of the transgenic eggplants. SmMYB35 could also bind to the promoters of SmCHS, SmF3H, SmDFR, and SmANS and enhance their activities. In addition, SmMYB35 interacted with SmTT8 and SmTTG1 to form a MBW complex which enhanced anthocyanin biosynthesis. Taking together, we firstly verified that SmMYB35 promoted anthocyanin biosynthesis in plants. The results provide new insights into the regulatory effects of SmMYB35 on key anthocyanin biosynthetic genes and advance our understanding of the molecular mechanism of light-induced anthocyanin synthesis in eggplants.

A novel transcription factor CmMYB012 inhibits flavone and anthocyanin biosynthesis in response to high temperatures in chrysanthemum

Flavones are among the major colorless pigments synthesized through branches of the flavonoid pathway in plants. However, due to the absence of a gene encoding flavone synthase (FNS) in the model plant Arabidopsis thaliana species, the regulatory mechanism of FNS-catalyzed flavone biosynthesis has rarely been studied in plants. Here, it was found that flavones play a predominant role in the elimination of excess reactive oxygen species (ROS) at high temperatures in colorless plant organs. A novel atypical subgroup 7 (SG7) R2R3-MYB transcription factor, CmMYB012, was found to be induced in response to prolonged high temperatures and to inhibit flavone biosynthesis by directly regulating CmFNS. Moreover, CmMYB012 was also found to inhibit anthocyanin biosynthesis by suppressing the expression of CmCHS, CmDFR, CmANS, and CmUFGT. CmMYB012 overexpression exerted a negative influence on plant fitness and pink flower color formation, while CmMYB012 suppression had the opposite effect in response to high temperatures. Our findings provide new insights into the mechanisms by which high temperatures regulate the metabolism of flavones and anthocyanins to affect plant fitness and flower color formation.

StWRKY13 promotes anthocyanin biosynthesis in potato (Solanum tuberosum) tubers

Although the role of WRKY transcription factors (TFs) in colour formation has been reported in several species, their function in potato (Solanum tuberosum L.) anthocyanin biosynthesis remains unclear. In this study, the potato WRKY gene StWRKY13 was isolated and characterised. Expression analysis revealed a significantly higher StWRKY13 expression in chromatic tubers than in yellow ones. Transient activation assays showed that StWRKY13 could enhance the role of StAN2 in promoting anthocyanin biosynthesis in tobacco (Nicotiana tabacum L.). Over-expressing the StWRKY13 gene promoted anthocyanin biosynthesis in potato tubers. Further investigations indicated that StWRKY13 could interact with the StCHS, StF3H, StDFR, and StANS gene promoters and significantly enhance their activities. Our findings showed that StWRKY13 could promote anthocyanin biosynthesis by activating StCHS, StF3H, StDFR, and StANS transcription in potato tubers, thereby supporting the theoretical basis for anthocyanins formation in coloured potato tubers.

Anthocyanins: From Mechanisms of Regulation in Plants to Health Benefits in Foods

Anthocyanins represent the major red, purple, and blue pigments in many flowers, fruits, vegetables, and cereals. They are also recognized as important health-promoting components in the human diet with protective effects against many chronic diseases, including cardiovascular diseases, obesity, and cancer. Anthocyanin biosynthesis has been studied extensively, and both biosynthetic and key regulatory genes have been isolated in many plant species. Here, we will provide an overview of recent progress in understanding the anthocyanin biosynthetic pathway in plants, focusing on the transcription factors controlling activation or repression of anthocyanin accumulation in cereals and fruits of different plant species, with special emphasis on the differences in molecular mechanisms between monocot and dicot plants. Recently, new insight into the transcriptional regulation of the anthocyanin biosynthesis, including positive and negative feedback control as well as epigenetic and post-translational regulation of MYB-bHLH-WD40 complexes, has been gained. We will consider how knowledge of regulatory mechanisms has helped to produce anthocyanin-enriched foods through conventional breeding and metabolic engineering. Additionally, we will briefly discuss the biological activities of anthocyanins as components of the human diet and recent findings demonstrating the important health benefits of anthocyanin-rich foods against chronic diseases.

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

Purple-fleshed sweetpotato (Ipomoea batatas（L.）Lam.) is rich in anthocyanins. R2R3-type MYB transcription factors（TFs）with EAR motifs inhibiting anthocyanin biosynthesis have been reported, and there is still a lack of information on how mutations in the EAR motifs of MYBs affect anthocyanin accumulation. In this study, we obtained three IbMYB44 TFs by bioinformatics. Among these TFs, IbMYB44.1, IbMYB44.3 with a complete EAR motif and IbMYB44.2 with a single amino acid mutant in the EAR motif caused an amino acid substitution from leucine to valine. RT-qPCR analysis showed that IbMYB44s was expressed at lower levels in the purple-fleshed sweetpotato than in nonpurple-fleshed sweetpotato (P < 0.01). Transient expression assays showed that the inhibitory effect of IbMYB44.1/3 was stronger than IbMYB44.2 in tobacco leaves and red-skinned pears. RT-qPCR analysis further proved that IbMYB44.1/3 significantly inhibited the expression of anthocyanin biosynthesis-related genes compared with IbMYB44.2 in tobacco leaves and red-skinned pears. A dual luciferase reporter assay showed that IbMYB44s cannot directly activate the IbANS promoter, and the result was also verified by yeast one-hybrid (Y1H) experiments. Moreover, we identified the interaction of IbMYB340 with IbMYB44.1, IbMYB44.2 and IbMYB44.3 via yeast two-hybrid (Y2H) assays. Thus, IbMYB44.1/3 could interact with IbMYB340 to negatively regulate anthocyanin biosynthesis. This study enriched the regulatory network of anthocyanins and also provided a theoretical basis for a single amino acid mutant from leucine to valine in the EAR motif of IbMYB44.2 affecting anthocyanin biosynthesis in the purple-fleshed sweetpotato.

Repressors of anthocyanin biosynthesis

Anthocyanins play a variety of adaptive roles in both vegetative tissues and reproductive organs of plants. The broad functionality of these compounds requires sophisticated regulation of the anthocyanin biosynthesis pathway to allow proper localization, timing, and optimal intensity of pigment deposition. While it is well-established that the committed steps of anthocyanin biosynthesis are activated by a highly conserved MYB-bHLH-WDR (MBW) protein complex in virtually all flowering plants, anthocyanin repression seems to be achieved by a wide variety of protein and small RNA families that function in different tissue types and in response to different developmental, environmental, and hormonal cues. In this review, we survey recent progress in the identification of anthocyanin repressors and the characterization of their molecular mechanisms. We find that these seemingly very different repression modules act through a remarkably similar logic, the so-called 'double-negative logic'. Much of the double-negative regulation of anthocyanin production involves signal-induced degradation or sequestration of the repressors from the MBW protein complex. We discuss the functional and evolutionary advantages of this logic design compared with simple or sequential positive regulation. These advantages provide a plausible explanation as to why plants have evolved so many anthocyanin repressors.