Overexpression of a grapevine R2R3-MYB factor in tomato affects vegetative development, flower morphology and flavonoid and terpenoid metabolism

A generalist regulator: MYB transcription factors regulate the biosynthesis of active compounds in medicinal plants

Medicinal plants are rich in a variety of secondary metabolites with therapeutic value. However, the yields of these metabolites are generally very low, making their extraction both time-consuming and labour-intensive. Transcription factor-targeted secondary metabolic engineering can efficiently regulate the biosynthesis and accumulation of secondary metabolites in medicinal plants. v-Myb avian myeloblastosis viral oncogene homolog (MYB) transcription factors are involved in regulating various morphological and developmental processes, responses to stress, and the biosynthesis of secondary metabolites in plants. This review discusses the biological functions and transcription regulation mechanisms of MYB transcription factors and summarizes research progress concerning MYB transcription factors involved in the biosynthesis of representative active components. In the transcriptional regulatory network, MYB transcription factors regulate multiple synthase genes to mediate the biosynthesis of active compounds. This work will serve as a reference for an in-depth analysis of the MYB transcription factor family in medicinal plants.

Plant terpenoid biosynthetic network and its multiple layers of regulation

Terpenoids constitute one of the largest and most chemically diverse classes of primary and secondary metabolites in nature with an exceptional breadth of functional roles in plants. Biosynthesis of all terpenoids begins with the universal five‑carbon building blocks, isopentenyl diphosphate (IPP) and its allylic isomer dimethylallyl diphosphate (DMAPP), which in plants are derived from two compartmentally separated but metabolically crosstalking routes, the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways. Here, we review the current knowledge on the terpenoid precursor pathways and highlight the critical hidden constraints as well as multiple regulatory mechanisms that coordinate and homeostatically govern carbon flux through the terpenoid biosynthetic network in plants.

CmBr confers fruit bitterness under CPPU treatment in melon

Many biotic or abiotic factors such as CPPU (N-(2-chloro-pyridin-4-yl)-N'-phenylurea), a growth regulator of numerous crops, can induce bitterness in cucurbits. In melon, cucurbitacin B is the major compound leading to bitterness. However, the molecular mechanism underlying CuB biosynthesis in response to different conditions remains unclear. Here, we identified a set of genes involved in CPPU-induced CuB biosynthesis in melon fruit and proposed CmBr gene as the major regulator. Using CRISPR/Cas9 gene editing, we confirmed CmBr's role in regulating CuB biosynthesis under CPPU treatment. We further discovered a CPPU-induced MYB-related transcription factor, CmRSM1, which specifically binds to the Myb motif within the CmBr promoter and activates its expression. Moreover, we developed an introgression line by introducing the mutated Cmbr gene into an elite variety and eliminated CPPU-induced bitterness, demonstrating its potential application in breeding. This study offers a valuable tool for breeding high-quality non-bitter melon varieties and provides new insights into the regulation of secondary metabolites under environmental stresses.

Overexpression of AtMYB12 transcription factor simultaneously enhances quercetin-dependent metabolites in radish callus

The study aimed to enhance quercetin production in radish by optimizing Agrobacterium tumefaciens-mediated in-planta transformation. This protocol involved infecting radish seed embryo axis with A. tumefaciens EHA105 strain carrying the 35S::AtMYB12. Radish seeds were infected with the Agrobacterium suspension (0.8 OD600) for 30 min, followed by sonication for 60 s and vacuum infiltration for 90 s at 100 mm Hg. A 3-day co-cultivation in Murashige and Skoog medium with 150 μM acetosyringone yielded a transformation efficiency of 59.6% and a transgenic callus induction rate of 32.3%. Transgenic plant and callus lines were confirmed by GUS histochemical assay, PCR, and qRT-PCR. The transgenic lines showed an increased expression of flavonoid pathway genes (AtMYB12, CHS, F3H, and FLS) and antioxidant genes (GPX, APX, CAT, and SOD) compared to WT plants. Overexpression of AtMYB12 in transgenic callus increased enzyme activity of phenylalanine ammonia lyase, catalase, and ascorbate peroxidase. In half-strength MS medium with 116.8 mM sucrose, the highest growth index (7.63) was achieved after 20 days. In AtMYB12 overexpressed callus lines, phenolic content (357.31 mg g-1 dry weight), flavonoid content (463 mg g-1 dry weight), and quercetin content (48.24 mg g-1 dry weight) increased significantly by 9.41-fold. Micro-wounding, sonication, and vacuum infiltration improved in-planta transformation in radishes. These high-quercetin-content transgenic callus lines hold promise as valuable sources of flavonoids.

Enhancement of specialized metabolites using CRISPR/Cas gene editing technology in medicinal plants

Plants are the richest source of specialized metabolites. The specialized metabolites offer a variety of physiological benefits and many adaptive evolutionary advantages and frequently linked to plant defense mechanisms. Medicinal plants are a vital source of nutrition and active pharmaceutical agents. The production of valuable specialized metabolites and bioactive compounds has increased with the improvement of transgenic techniques like gene silencing and gene overexpression. These techniques are beneficial for decreasing production costs and increasing nutritional value. Utilizing biotechnological applications to enhance specialized metabolites in medicinal plants needs characterization and identification of genes within an elucidated pathway. The breakthrough and advancement of CRISPR/Cas-based gene editing in improving the production of specific metabolites in medicinal plants have gained significant importance in contemporary times. This article imparts a comprehensive recapitulation of the latest advancements made in the implementation of CRISPR-gene editing techniques for the purpose of augmenting specific metabolites in medicinal plants. We also provide further insights and perspectives for improving metabolic engineering scenarios in medicinal plants.

Beyond skin-deep: targeting the plant surface for crop improvement

The above-ground plant surface is a well-adapted tissue layer that acts as an interface between the plant and its surrounding environment. As such, its primary role is to protect against desiccation and maintain the gaseous exchange required for photosynthesis. Further, this surface layer provides a barrier against pathogens and herbivory, while attracting pollinators and agents of seed dispersal. In the context of agriculture, the plant surface is strongly linked to post-harvest crop quality and yield. The epidermal layer contains several unique cell types adapted for these functions, while the non-lignified above-ground plant organs are covered by a hydrophobic cuticular membrane. This review aims to provide an overview of the latest understanding of the molecular mechanisms underlying crop cuticle and epidermal cell formation, with focus placed on genetic elements contributing towards quality, yield, drought tolerance, herbivory defence, pathogen resistance, pollinator attraction, and sterility, while highlighting the inter-relatedness of plant surface development and traits. Potential crop improvement strategies utilizing this knowledge are outlined in the context of the recent development of new breeding techniques.

Recent advances in triterpenoid pathway elucidation and engineering

Triterpenoids are among the most assorted class of specialized metabolites found in all the taxa of living organisms. Triterpenoids are the leading active ingredients sourced from plant species and are utilized in pharmaceutical and cosmetic industries. The triterpenoid precursor 2,3-oxidosqualene, which is biosynthesized via the mevalonate (MVA) pathway is structurally diversified by the oxidosqualene cyclases (OSCs) and other scaffold-decorating enzymes such as cytochrome P450 monooxygenases (P450s), UDP-glycosyltransferases (UGTs) and acyltransferases (ATs). A majority of the bioactive triterpenoids are harvested from the native hosts using the traditional methods of extraction and occasionally semi-synthesized. These methods of supply are time-consuming and do not often align with sustainability goals. Recent advancements in metabolic engineering and synthetic biology have shown prospects for the green routes of triterpenoid pathway reconstruction in heterologous hosts such as Escherichia coli, Saccharomyces cerevisiae and Nicotiana benthamiana, which appear to be quite promising and might lead to the development of alternative source of triterpenoids. The present review describes the biotechnological strategies used to elucidate complex biosynthetic pathways and to understand their regulation and also discusses how the advances in triterpenoid pathway engineering might aid in the scale-up of triterpenoid production in engineered hosts.

Global dissection of R2R3-MYB in Pogostemon cablin uncovers a species-specific R2R3-MYB clade

MYB family is one of the largest transcription factor families in plants and plays a crucial role in regulating plant biochemical and physiological processes. However, R2R3-MYBs in patchouli have not been systematically investigated. Here, based on the gene annotation of patchouli genome sequence, 484 R2R3-MYB transcripts were detected. Further in-depth analysis of the gene structure and expression of R2R3-MYBs supported the tetraploid hybrid origin of patchouli. When combined with R2R3-MYBs from Arabidopsis, a phylogenetic tree of patchouli R2R3-MYBs was constructed and divided into 31 clades. Interestingly, a patchouli-specific R2R3-MYB clade was found and confirmed by homologous from other Lamiaceae species. The syntenic analysis demonstrated that tandem duplication contributed to its evolution. This study systematically analysed the R2R3-MYB family in patchouli, providing information on its gene characterization, functional prediction, and species evolution.

Composition, metabolism and postharvest function and regulation of fruit cuticle: A review

The cuticle of plants, a hydrophobic membrane that covers their aerial organs, is crucial to their ability to withstand biotic and abiotic stressors. Fruit is the reproductive organ of plants, and an important dietary source that can offer a variety of nutrients for the human body, and fruit cuticle performs a crucial protective role in fruit development and postharvest quality. This review discusses the universality and diversity of the fruit cuticle composition, and systematically summarizes the metabolic process of fruit cuticle, including the biosynthesis, transport and regulatory factors (including transcription factors, phytohormones and environmental elements) of fruit cuticle. Additionally, we emphasize the postharvest functions and postharvest regulatory technologies of fruit cuticle, and propose future research directions for fruit cuticle.

AgMYB5, an MYB transcription factor from celery, enhanced β-carotene synthesis and promoted drought tolerance in transgenic Arabidopsis

BACKGROUND

Water shortage caused by global warming seriously affects the yield and quality of vegetable crops. β-carotene, the lipid-soluble natural product with important pharmacological value, is abundant in celery. Transcription factor MYB family extensively disperses in plants and plays regulatory roles in carotenoid metabolism and water scarcity response.

RESULTS

Here, the AgMYB5 gene encoding 196 amino acids was amplified from celery cv. 'Jinnanshiqin'. In celery, the expression of AgMYB5 exhibited transactivation activity, tissue specificity, and drought-condition responsiveness. Further analysis proved that ectopic expression of AgMYB5 increased β-carotene content and promoted drought tolerance in transgenic Arabidopsis thaliana. Moreover, AgMYB5 expression promoted β-carotene biosynthesis by triggering the expression of AtCRTISO and AtLCYB, which in turn increased antioxidant enzyme activities, and led to the decreased contents of H₂O₂ and MDA, and the inhibition of O₂^- generation. Meanwhile, β-carotene accumulation promoted endogenous ABA biosynthesis of transgenic Arabidopsis, which resulted in ABA-induced stomatal closing and delayed water loss. In addition, ectopic expression of AgMYB5 increased expression levels of AtERD1, AtP5CS1, AtRD22, and AtRD29.

CONCLUSIONS

The findings indicated that AgMYB5 up-regulated β-carotene biosynthesis and drought tolerance of Arabidopsis.

The SmMYB36-SmERF6/SmERF115 module regulates the biosynthesis of tanshinones and phenolic acids in salvia miltiorrhiza hairy roots

Tanshinone and phenolic acids are the most important active substances of Salvia miltiorrhiza, and the insight into their transcriptional regulatory mechanisms is an essential process to increase their content in vivo. SmMYB36 has been found to have important regulatory functions in the synthesis of tanshinone and phenolic acid; paradoxically, its mechanism of action in S. miltiorrhiza is not clear. Here, we demonstrated that SmMYB36 functions as a promoter of tanshinones accumulation and a suppressor of phenolic acids through the generation of SmMYB36 overexpressed and chimeric SmMYB36-SRDX (EAR repressive domain) repressor hairy roots in combination with transcriptomic-metabolomic analysis. SmMYB36 directly down-regulate the key enzyme gene of primary metabolism, SmGAPC, up-regulate the tanshinones biosynthesis branch genes SmDXS2, SmGGPPS1, SmCPS1 and down-regulate the phenolic acids biosynthesis branch enzyme gene, SmRAS. Meanwhile, SmERF6, a positive regulator of tanshinone synthesis activating SmCPS1, was up-regulated and SmERF115, a positive regulator of phenolic acid biosynthesis activating SmRAS, was down-regulated. Furthermore, the seven acidic amino acids at the C-terminus of SmMYB36 are required for both self-activating domain and activation of target gene expression. As a consequence, this study contributes to reveal the potential relevance of transcription factors synergistically regulating the biosynthesis of tanshinone and phenolic acid.

MYB transcription factors and their role in Medicinal plants

Transcription factors are multi-domain proteins that regulate gene expression in eukaryotic organisms. They are one of the largest families of proteins, which are structurally and functionally diverse. While there are transcription factors that are plant-specific, such as AP2/ERF, B3, NAC, SBP and WRKY, some transcription factors are present in both plants as well as other eukaryotic organisms. MYB transcription factors are widely distributed among all eukaryotes. In plants, the MYB transcription factors are involved in the regulation of numerous functions such as gene regulation in different metabolic pathways especially secondary metabolic pathways, regulation of different signalling pathways of plant hormones, regulation of genes involved in various developmental and morphological processes etc. Out of the thousands of MYB TFs that have been studied in plants, the majority of them have been studied in the model plants like Arabidopsis thaliana, Oryza sativa etc. The study of MYBs in other plants, especially medicinal plants, has been comparatively limited. But the increasing demand for medicinal plants for the production of biopharmaceuticals and important bioactive compounds has also increased the need to explore more number of these multifaceted transcription factors which play a significant role in the regulation of secondary metabolic pathways. These studies will ultimately contribute to medicinal plants' research and increased production of secondary metabolites, either through transgenic plants or through synthetic biology approaches. This review compiles studies on MYB transcription factors that are involved in the regulation of diverse functions in medicinal plants.

Structural and interactions analysis of a transcription factor PnMYB2 in Panax notoginseng

The main active ingredients of the traditional Chinese medicinal plant, Panax notoginseng, are the Panax notoginseng saponins (PNS). They can be synthesized via the mevalonate pathway; PnSS and PnSE1 are the key rate-limiting enzymes in this pathway. In this study, an interaction between PnMYB2 and the key enzymes was identified and characterized from the P. notoginseng cDNA library using the Y1H technique. Subsequently, X-α-gal color reaction confirmed the interaction between PnMYB2 and the upstream sequences of PnSS and PnSE1 promoters. Full-length cDNA sequence of PnMYB2 was isolated and characterized. PnMYB2 has an open reading frame of 864 bp, encoding 287 amino acids. 3D structural analysis of PnMYB2 indicated that its structure was similar to that of the template. Phylogenetic analysis revealed that PnMYB2 and PgMYB2 are highly homologous and belong to the R2R3 MYB transcription factor (TF). Subcellular localization analysis showed that PnMYB2 was localized in the nucleus. The recombinant protein PnMYB2 was successfully obtained through prokaryotic expression and was confirmed to be an inclusion body protein. Furthermore, electrophoretic mobility shift assay (EMSA) experiments demonstrated that PnMYB2 specifically binds to MYB core and AC-rich elements. This study provides a theoretical basis for transcriptional regulation of saponin biosynthesis in P. notoginseng.

Whole-Genome Identification and Analysis of Multiple Gene Families Reveal Candidate Genes for Theasaponin Biosynthesis in Camellia oleifera

Camellia oleifera is an economically important oilseed tree. Seed meals of C. oleifera have a long history of use as biocontrol agents in shrimp farming and as cleaning agents in peoples’ daily lives due to the presence of theasaponins, the triterpene saponins from the genus Camellia. To characterize the biosynthetic pathway of theasaponins in C. oleifera, members of gene families involved in triterpenoid biosynthetic pathways were identified and subjected to phylogenetic analysis with corresponding members in Arabidopsis thaliana, Camellia sinensis, Actinidia chinensis, Panax ginseng, and Medicago truncatula. In total, 143 triterpenoid backbone biosynthetic genes, 1169 CYP450s, and 1019 UGTs were identified in C. oleifera. The expression profiles of triterpenoid backbone biosynthetic genes were analyzed in different tissue and seed developmental stages of C. oleifera. The results suggested that MVA is the main pathway for triterpenoid backbone biosynthesis. Moreover, the candidate genes for theasaponin biosynthesis were identified by WGCNA and qRT-PCR analysis; these included 11 CYP450s, 14 UGTs, and eight transcription factors. Our results provide valuable information for further research investigating the biosynthetic and regulatory network of theasaponins.

Application of metabolic engineering to enhance the content of alkaloids in medicinal plants

Plants are a rich source of bioactive compounds, many of which have been exploited for cosmetic, nutritional, and medicinal purposes. Through the characterization of metabolic pathways, as well as the mechanisms responsible for the accumulation of secondary metabolites, researchers have been able to increase the production of bioactive compounds in different plant species for research and commercial applications. The intent of the current review is to describe the metabolic engineering methods that have been used to transform in vitro or field-grown medicinal plants over the last decade and to identify the most effective approaches to increase the production of alkaloids. The articles summarized were categorized into six groups: endogenous enzyme overexpression, foreign enzyme overexpression, transcription factor overexpression, gene silencing, genome editing, and co-overexpression. We conclude that, because of the complex and multi-step nature of biosynthetic pathways, the approach that has been most commonly used to increase the biosynthesis of alkaloids, and the most effective in terms of fold increase, is the co-overexpression of two or more rate-limiting enzymes followed by the manipulation of regulatory genes.

Transcriptomic profiling of the floral fragrance biosynthesis pathway of Liriodendron and functional characterization of the LtuDXR gene

Floral fragrance, which has the function of attracting pollinators, is a class of volatile secondary metabolites mainly released by the secretory tissue of petals. Terpenoids are key components of floral volatile substances. Previous studies have shown that there are significant differences in the concentration and composition of volatile floral fragrances, especially terpenoids, between Liriodendron chinense and L. tulipifera. At present, the mechanism by which the synthesis of floral fragrance is regulated in Liriodendron remains unexplored. In this study, we analyzed the differentially expressed genes (DEGs) of L. chinense and L. tulipifera, and identified 130 DEGs related to terpenoid synthesis. A KEGG enrichment analysis of DEGs related to terpenoid biosynthesis revealed that the monoterpenoid biosynthesis pathway was the most significant. We cloned the LtuDXR gene from L. tulipifera using RACE technology. RT-qPCR results showed that the expression of the LtuDXR gene was the highest in the early florescence petals, indicating that the LtuDXR gene may play a role in the synthesis of volatile terpenoids. Subcellular localization showed that the LtuDXR protein is mainly localized in the chloroplast. Overexpression of LtuDXR in Arabidopsis thaliana significantly increased the plant height, DXR enzyme activity, and carotenoid content. In this study, we identified and functionally characterized LtuDXR, which is involved in terpenoid synthesis in Liriodendron. Our work lays the foundation for further exploration of the molecular mechanism by which terpenoid biosynthesis is regulated in Liriodendron.

PtrMYB120 functions as a positive regulator of both anthocyanin and lignin biosynthetic pathway in a hybrid poplar

Both anthocyanins and lignins are essential secondary metabolites in plant growth and development. Their biosynthesis is metabolically interconnected and diverges in the central metabolite 4-coumaroyl CoA of the phenylpropanoid pathway. Considerable progress has been made in understanding transcriptional regulation of genes involved in lignin and anthocyanin synthesis pathways, but the concerted regulation of these pathways is not yet fully understood. Here, we functionally characterized PtrMYB120, a R2R3-MYB transcription factor from Populus trichocarpa. Overexpression of PtrMYB120 in a hybrid poplar (i.e., 35S::PtrMYB120) was associated with increased anthocyanin (i.e., cyanidin 3-O-glucoside) accumulation and upregulation of anthocyanin biosynthetic genes. However, transgenic poplars with dominant suppression of PtrMYB120 function achieved by fusing the ERF-associated amphiphilic repression motif to PtrMYB120 (i.e., 35S::PtrMYB120-SRDX) had a dramatic decrease in not only anthocyanin but also Klason lignin content with downregulation of both anthocyanin and lignin biosynthetic genes. Indeed, 35S::PtrMYB120-SRDX poplars had irregularly shaped xylem vessels with reduced S-lignin content in stems, which was proportionally related to the level of the introduced PtrMYB120-SRDX gene. Furthermore, protoplast-based transcriptional activation assay using the PtrMYB120-GR system suggested that PtrMYB120 directly regulates genes involved in both anthocyanin and lignin biosynthesis, including chalcone synthase and ferulate-5 hydroxylase. Interestingly, the saccharification efficiency of line #6 of 35S::PtrMYB120-SRDX poplars, which had slightly reduced lignin content with a normal growth phenotype, was dramatically enhanced (>45%) by NaOH treatment. Taken together, our results suggest that PtrMYB120 functions as a positive regulator of both anthocyanin and lignin biosynthetic pathways and can be targeted to enhance saccharification efficiency in woody perennials.

Genome-Wide Analysis Reveals the Potential Role of MYB Transcription Factors in Floral Scent Formation in Hedychium coronarium

The MYB gene family is one of the largest groups of transcription factors (TFs) playing diverse roles in several biological processes. Hedychium coronarium (white ginger lily) is a renowned ornamental plant both in tropical and subtropical regions due to its flower shape and strong floral scent mainly composed of terpenes and benzenoids. However, there is no information available regarding the role of the MYB gene family in H. coronarium. In the current study, the MYB gene family was identified and extensively analyzed. The identified 253 HcMYB genes were unevenly mapped on 17 chromosomes at a different density. Promoter sequence analysis showed numerous phytohormones related to cis-regulatory elements. The majority of HcMYB genes contain two to three introns and motif composition analysis showed their functional conservation. Phylogenetic analysis revealed that HcMYBs could be classified into 15 distinct clades, and the segmental duplication events played an essential role in the expansion of the HcMYB gene family. Tissue-specific expression patterns of HcMYB genes displayed spatial and temporal expression. Furthermore, seven HcMYB (HcMYB7/8/75/79/145/238/248) were selected for further investigation. Through RT-qPCR, the response of candidates HcMYB genes toward jasmonic acid methyl ester (MeJA), abscisic acid (ABA), ethylene, and auxin was examined. Yeast one-hybrid (Y1H) assays revealed that candidate genes directly bind to the promoter of bottom structural volatile synthesis genes (HcTPS1, HcTPS3, HcTPS10, and HcBSMT2). Moreover, yeast two-hybrid (Y2H) assay showed that HcMYB7/8/75/145/248 interact with HcJAZ1 protein. In HcMYB7/8/79/145/248-silenced flowers, the floral volatile contents were decreased and downregulated the expression of key structural genes, suggesting that these genes might play crucial roles in floral scent formation in H. coronarium by regulating the expression of floral scent biosynthesis genes. Collectively, these findings indicate that HcMYB genes might be involved in the regulatory mechanism of terpenoids and benzenoid biosynthesis in H. coronarium.

Towards Sensor-Based Phenotyping of Physical Barriers of Grapes to Improve Resilience to Botrytis Bunch Rot

Botrytis bunch rot is one of the economically most important fungal diseases in viticulture (aside from powdery mildew and downy mildew). So far, no active defense mechanisms and resistance loci against the necrotrophic pathogen are known. Since long, breeders are mostly selecting phenotypically for loose grape bunches, which is recently the most evident trait to decrease the infection risk of Botrytis bunch rot. This study focused on plant phenomics of multiple traits by applying fast sensor technologies to measure berry impedance (Z _REL ), berry texture, and 3D bunch architecture. As references, microscopic determined cuticle thickness (MS _CT ) and infestation of grapes with Botrytis bunch rot were used. Z _REL hereby is correlated to grape bunch density OIV204 (r = -0.6), cuticle thickness of berries (r = 0.61), mean berry diameter (r = -0.63), and Botrytis bunch rot (r = -0.7). However, no correlation between Z _REL and berry maturity or berry texture was observed. In comparison to the category of traditional varieties (mostly susceptible), elite breeding lines show an impressive increased Z _REL value (+317) and a 1-μm thicker berry cuticle. Quantitative trait loci (QTLs) on LGs 2, 6, 11, 15, and 16 were identified for Z _REL and berry texture explaining a phenotypic variance of between 3 and 10.9%. These QTLs providing a starting point for the development of molecular markers. Modeling of Z _REL and berry texture to predict Botrytis bunch rot resilience revealed McFadden R ² = 0.99. Taken together, this study shows that in addition to loose grape bunch architecture, berry diameter, Z _REL , and berry texture values are probably additional parameters that could be used to identify and select Botrytis-resilient wine grape varieties. Furthermore, grapevine breeding will benefit from these reliable methodologies permitting high-throughput screening for additional resilience traits of mechanical and physical barriers to Botrytis bunch rot. The findings might also be applicable to table grapes and other fruit crops like tomato or blueberry.

The MYB transcription factor CiMYB42 regulates limonoids biosynthesis in citrus

BACKGROUND

Limonoids are major bioactive compounds that are produced by the triterpenoid metabolic pathway. The detailed biochemical process of limonoid biosynthesis and the mechanism of its molecular regulation remain elusive. The identification of transcription factors that regulate limonoid biosynthetic pathways is very important for understanding the underlying regulatory mechanisms. This information could also provide tools for manipulating biosynthesis genes to modulate limonoid production.

RESULTS

In this study, the CiMYB42 transcription factor was isolated to identify its role in limonoid biosynthesis. Multiple alignment analysis and phylogenetic analysis demonstrated that CiMYB42 is a typical R2R3MYB transcription factor that shares high similarity of its amino acid sequence with AtMYB42. Limonoids contents were higher in Citrus sinensis and Citrus grandis than in other species. Limonoid accumulation during leaf development also showed diverse trends in different genotypes. The expression of CiMYB42 was significantly related to the limonoid content and the expression of CiOSC in some citrus accessions. The overexpression of CiMYB42 in sweet orange resulted in significant accumulation of limonin, whereas the downregulation of CiMYB42 by RNAi resulted in a dwarf phenotype and less nomilin accumulation. Furthermore, the results of a yeast one-hybrid assay and EMSA indicated that CiMYB42 binds exclusively to the TTGTTG sequence (type II MYB core) in the promoter of CiOSC. Together, these results suggest that CiMYB42 positively regulates limonoid biosynthesis by regulating the expression of CiOSC by binding to the TTGTTG sequence (type II MYB core) of its promoter.

CONCLUSIONS

CiMYB42 is an important transcription activator involved in limonoid biosynthesis that regulates the expression of CiOSC by binding to the TTGTTG sequence (type II MYB core).

Parallel Transcriptional Regulation of Artemisinin and Flavonoid Biosynthesis

Plants regulate the synthesis of specialized compounds through the actions of individual transcription factors (TFs) or sets of TFs. One such compound, artemisinin from Artemisia annua, is widely used as a pharmacological product in the first-line treatment of malaria. However, the emergence of resistance to artemisinin in Plasmodium species, as well as its low production rates, have required innovative treatments such as exploiting the synergistic effects of flavonoids with artemisinin. We overview current knowledge about flavonoid and artemisinin transcriptional regulation in A. annua, and review the dual action of TFs and structural genes that can regulate both pathways simultaneously. Understanding the concerted action of these TFs and their associated structural genes can guide the development of strategies to further improve flavonoid and artemisinin production.

CmMYB8 encodes an R2R3 MYB transcription factor which represses lignin and flavonoid synthesis in chrysanthemum

R2R3-MYB transcription factors are important regulators of the growth and development of plants. Here, CmMYB8 a chrysanthemum gene encoding an R2R3-MYB transcription factor, was isolated and functionally characterized. The gene was transcribed throughout the plant, but most strongly in the stem. When CmMYB8 was over-expressed, a number of genes encoding components of lignin synthesis were down-regulated, and the plants' lignin content was reduced. The composition of the lignin in the transgenic plants was also altered, and its S/G ratio was reduced. A further consequence of the over-expression of CmMYB8 was to lessen the transcript abundance of key genes involved in flavonoid synthesis, resulting in a reduced accumulation of flavonoids. The indication is that the CmMYB8 protein participates in the negative regulation of both lignin and flavonoid synthesis.

Genome-Wide Identification, Classification, and Expression Profiling Reveals R2R3-MYB Transcription Factors Related to Monoterpenoid Biosynthesis in Osmanthus fragrans

Osmanthus fragrans is widely grown for the purpose of urban greening and the pleasant aroma emitted from its flowers. The floral scent is determined by several monoterpenoid volatiles, such as linalool and its oxides, which are a few of the most common volatiles and the main components of the essential oils in most sweet osmanthus cultivars. In addition, the relative contents of cis- and trans-linalool oxide (furan) may affect the aromas and quality of the essential oils. MYB proteins represent the largest family of transcription factors in plants and participate in regulating secondary metabolites. Several cis-elements, especially AC-rich regions, are known to be bound by 2R-MYBs and could be found in the promoter of the enzyme genes in the terpenoid metabolic pathway. However, there has to date been no investigation into the 2R-MYB family genes involved in regulating terpenoid biosynthesis in O. fragrans. Here, 243 non-redundant 2R-MYB proteins were grouped into 33 clusters based on the phylogeny and exon-intron distribution. These genes were unevenly distributed on 23 chromosomes. Ka/Ks analysis showed that the major mode of 2R-MYB gene evolution was purifying selection. Expression analysis indicated that 2R-MYB genes in O. fragrans exhibited varied expression patterns. A total of 35 OfMYBs representing the highest per kilobase per million mapped reads in the flower were selected for quantitative real-time PCR analysis. The correlation analysis between the expression level and the contents of fragrant compounds at different flowering stages suggested that OfMYB19/20 exhibited remarkably positive correlation with the accumulation of cis-linalool oxides. OfMYB51/65/88/121/137/144 showed significantly negative correlations with one or more linalool oxides. Characterization of these proteins revealed that OfMYB19 and OfMYB137 were localized in the nuclei, but did not show transcriptional activation in the yeast system, which suggested that they may be bound to other transcription factors to exert regulatory functions. These findings provide useful information for further functional investigation of the 2R-MYBs and offer a foundation for clarifying the 2R-MYB transcription factors involved in the molecular mechanism of the regulation of monoterpenoid biosynthesis in Osmanthus fragrans.

RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics

BACKGROUND

Flavonoids are produced in all flowering plants in a wide range of tissues including in berry fruits. These compounds are of considerable interest for their biological activities, health benefits and potential pharmacological applications. However, transcriptomic and genomic resources for wild and cultivated berry fruit species are often limited, despite their value in underpinning the in-depth study of metabolic pathways, fruit ripening as well as in the identification of genotypes rich in bioactive compounds.

RESULTS

To access the genetic diversity of wild and cultivated berry fruit species that accumulate high levels of phenolic compounds in their fleshy berry(-like) fruits, we selected 13 species from Europe, South America and Asia representing eight genera, seven families and seven orders within three clades of the kingdom Plantae. RNA from either ripe fruits (ten species) or three ripening stages (two species) as well as leaf RNA (one species) were used to construct, assemble and analyse de novo transcriptomes. The transcriptome sequences are deposited in the BacHBerryGEN database (http://jicbio.nbi.ac.uk/berries) and were used, as a proof of concept, via its BLAST portal (http://jicbio.nbi.ac.uk/berries/blast.html) to identify candidate genes involved in the biosynthesis of phenylpropanoid compounds. Genes encoding regulatory proteins of the anthocyanin biosynthetic pathway (MYB and basic helix-loop-helix (bHLH) transcription factors and WD40 repeat proteins) were isolated using the transcriptomic resources of wild blackberry (Rubus genevieri) and cultivated red raspberry (Rubus idaeus cv. Prestige) and were shown to activate anthocyanin synthesis in Nicotiana benthamiana. Expression patterns of candidate flavonoid gene transcripts were also studied across three fruit developmental stages via the BacHBerryEXP gene expression browser (http://www.bachberryexp.com) in R. genevieri and R. idaeus cv. Prestige.

CONCLUSIONS

We report a transcriptome resource that includes data for a wide range of berry(-like) fruit species that has been developed for gene identification and functional analysis to assist in berry fruit improvement. These resources will enable investigations of metabolic processes in berries beyond the phenylpropanoid biosynthetic pathway analysed in this study. The RNA-seq data will be useful for studies of berry fruit development and to select wild plant species useful for plant breeding purposes.

Transcriptome Analysis of Clinopodium chinense (Benth.) O. Kuntze and Identification of Genes Involved in Triterpenoid Saponin Biosynthesis

Clinopodium chinense (Benth.) O. Kuntze (C. chinense) is an important herb in traditional Chinese medicine. Triterpenoid saponins are a major class of active compounds in C. chinense with broad pharmacological activities and hemostatic, antitumor, and anti-hyperglycemic effects. To identify genes involved in triterpenoid saponin biosynthesis, transcriptomic analyses of leaves, stems, and roots from C. chinense were performed. A total of 135,968 unigenes were obtained by assembling the leaf, stem, and root transcripts, of which 102,154 were annotated in public databases. Differentially expressed genes were determined based on expression profile analysis and analyzed for differential expression of unique genes related to triterpenoid saponin biosynthesis. Multiple unigenes encoding crucial enzymes or transcription factors involved in triterpenoid saponin synthesis were identified and analyzed. The expression levels of unigenes encoding enzymes were experimentally validated using quantitative real-time PCR. This study greatly broadens the public transcriptome database for this species and provides a valuable resource for identifying candidate genes involved in the biosynthesis of triterpenoid saponins and other secondary metabolites.

PgMYB2, a MeJA-Responsive Transcription Factor, Positively Regulates the Dammarenediol Synthase Gene Expression in Panax Ginseng

The MYB transcription factor family members have been reported to play different roles in plant growth regulation, defense response, and secondary metabolism. However, MYB gene expression has not been reported in Panax ginseng. In this study, we isolated a gene from ginseng adventitious root, PgMYB2, which encodes an R2R3-MYB protein. Subcellular localization revealed that PgMYB2 protein was exclusively detected in the nucleus of Allium cepa epidermis. The highest expression level of PgMYB2 was found in ginseng root and it was significantly induced by plant hormones methyl jasmonate (MeJA). Furthermore, the binding interaction between PgMYB2 protein and the promoter of dammarenediol synthase (DDS) was found in the yeast strain Y1H Gold. Moreover, the electrophoretic mobility shift assay (EMSA) identified the binding site of the interaction and the results of transiently overexpressing PgMYB2 in plants also illustrated that it may positively regulate the expression of PgDDS. Based on the key role of PgDDS gene in ginsenoside synthesis, it is reasonable to believe that this report will be helpful for the future studies on the MYB family in P. ginseng and ultimately improving the ginsenoside production through genetic and metabolic engineering.

CtACO1 Overexpression Resulted in the Alteration of the Flavonoids Profile of Safflower

Background: Flavonoids with various structures play a vital role in plant acclimatization to varying environments as well as in plant growth, development, and reproduction. Exogenous applications of ethylene and 1-aminocyclopropane carboxylic acid (ACC), could affect the accumulation of flavonoids. Very few attempts have been made to investigate the effect of 1-aminocyclopropane carboxylic acid oxidase (ACO), a unique enzyme that catalyzes ACC to ethylene, on genes and metabolites in the flavonoid biosynthetic pathway. In this study, two ACOs in safflower (CtACOs) were cloned, and then transgenic safflower with overexpressed CtACO1 was generated through the Agrobacterium-mediated floral dipping method. Results: CtACO1 and CtACO2 were both characterized by the 2-oxoglutarate binding domain RxS and the ferrous iron binding site HxDxnH as ACOs from other plants. However, the transcript levels of CtACO1 in flowers at stages I, II, III, and IV were all higher than those of CtACO2. At the cellular level, by using electroporation transformation, CtACO1 was found to be localized at the cytomembrane in onion epidermal cells. CtACO1 overexpression had varying effects on genes involved in the ethylene and flavonoid biosynthetic pathways. The metabolites analysis showed that CtACO1 overexpression lines had a higher accumulation of quercetin and its glycosylated derivatives (quercetin 3-β-d-glucoside and rutin). In contrast, the accumulation of quinochalcones (hydroxysafflor yellow A and carthamin), kaempferol glycosylated derivatives (kaempferol-3-O-β-rutinoside and kaempferol-3-O-β-d-glucoside), apigenin, and luteolin in CtACO1 overexpression lines were decreased. Conclusion: This study confirmed the feasibility of applying the floral dipping method to safflower and showed a novel regulatory effect of CtACO1 in the flavonoid biosynthetic pathway. It provides hypothetical and practical groundwork for further research on regulating the overall metabolic flux of flavonoids in safflower, particularly hydroxysafflor yellow A and other quinochalcones, by using appropriate genetic engineering strategies.

GmMYB181, a Soybean R2R3-MYB Protein, Increases Branch Number in Transgenic Arabidopsis

Soybean (Glycine max) is an important economic crop that provides abundant oil and high quality protein for human beings. As the process of reproductive growth directly determines the crop seed yield and quality, we initiated studies to identify genes that regulate soybean floral organ development. One R2R3-MYB transcription factor gene, designated as GmMYB181, was found to be enriched in flowers based on microarray analysis and was further functionally investigated in transgenic Arabidopsis. GmMYB181 protein contains two MYB domains, which localized to the nucleus and displayed transcriptional activation in yeast hybrid system. Real-time quantitative PCR (qRT-PCR) results suggested GmMYB181 exclusively expressed in flower tissue. In Arabidopsis, overexpression of GmMYB181 altered the morphology of floral organs, fruit size and plant architecture, including outward curly sepals, smaller siliques, increased lateral branches and reduced plant height, indicating that GmMYB181 is involved in the development of reproductive organs and plays an important role in controlling plant architecture. Further, microarray analysis revealed that overexpressing GmMYB181 in Arabidopsis affected the expression of 3450 genes in mature flowers, including those involved in floral organ, seed/fruit development, and responded to different hormone signals.

Kiwifruit R2R3-MYB transcription factors and contribution of the novel AcMYB75 to red kiwifruit anthocyanin biosynthesis

Red kiwifruit (Actinidia chinensis) is a popular fresh fruit with a high market value due to its unique color, caused by anthocyanin accumulation. The R2R3-MYB transcription factors (TFs) have important roles in plant development and anthocyanin metabolism. In this first comprehensive study of R2R3-MYBs in kiwifruit, a total of 93 R2R3-MYB genes, including five novel previously unannotated AcMYBs, were identified. Their phylogenic relationship, exon-intron structures, and conserved motifs were analyzed. Based on transcriptome data, 60 AcMYBs were expressed (FPKM > 1) across seven developmental stages of kiwifruit, revealing five expression patterns. One of the 5 newly identified R2R3 TFs, AcMYB75, showed an anthocyanin accumulation-linked expression pattern during fruit development. AcMYB75 localized to the nucleus and has an active transactivation domain, verifying it as a transcription factor. AcMYB75 protein specifically bound the promoter of the anthocyanin biosynthesis gene ANS in yeast one-hybrid system and in vivo. In 35 S:AcMYB75 Arabidopsis plants, anthocyanin significantly accumulated in leaves, and the expression of anthocyanin biosynthetic genes was greatly up-regulated. Together, these results suggest that AcMYB75 is involved in anthocyanin biosynthesis in kiwifruit. These findings will increase our understanding of AcMYBs involved in anthocyanin biosynthesis, and also benefit further functional characterization of R2R3-MYB genes in kiwifruit.

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.

Enhancing diterpenoid concentration in Salvia miltiorrhiza hairy roots through pathway engineering with maize C1 transcription factor

Tanshinones are valuable natural diterpenoids from danshen (Salvia miltiorrhiza Bunge). Here, it was demonstrated that maize transcription factor C1 improved the accumulation of tanshinones by comprehensively upregulating the pathway genes, especially SmMDC and SmPMK in danshen hairy roots, yielding total tanshinones up to 3.59mg g(-1) of dry weight in line C1-6, a 3.4-fold increase compared with the control. Investigation of 2024bp of the SmMDC promoter fragment revealed that C1-mediated upregulation of terpenoid genes was possibly due to the direct interaction of C1 with its recognition sequences. The increase of tanshinones was accompanied by a decrease of salvianolic acid production, the other bioactive ingredient in danshen, by up to 37% compared with the control. This was the result of the downregulation of SmTAT, the entry-point gene of the tyrosine pathway, which promoted metabolic flow to anthocyanins rather than to salvianolic acids. Based on the findings of the present study, it was concluded that cis-acting elements shared by terpenoid and phenylpropanoid biosynthetic genes are partially responsible for the C1-stimulated variation of tanshinone and salvianolic acid concentrations.

De Novo Transcriptome Sequencing of the Orange-Fleshed Sweet Potato and Analysis of Differentially Expressed Genes Related to Carotenoid Biosynthesis

Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop worldwide. The orange-fleshed sweet potato is considered to be an important source of beta-carotene. In this study, the transcriptome profiles of an orange-fleshed sweet potato cultivar “Weiduoli” and its mutant “HVB-3” with high carotenoid content were determined by using the high-throughput sequencing technology. A total of 13,767,387 and 9,837,090 high-quality reads were produced from Weiduoli and HVB-3, respectively. These reads were de novo assembled into 58,277 transcripts and 35,909 unigenes with an average length of 596 bp and 533 bp, respectively. In all, 874 differentially expressed genes (DEGs) were obtained between Weiduoli and HVB-3, 401 of which were upregulated and 473 were downregulated in HVB-3 compared to Weiduoli. Of the 697 DEGs annotated, 316 DEGs had GO terms and 62 DEGs were mapped onto 50 pathways. The 22 DEGs and 31 transcription factors involved in carotenoid biosynthesis were identified between Weiduoli and HVB-3. In addition, 1,725 SSR markers were detected. This study provides the genomic resources for discovering the genes involved in carotenoid biosynthesis of sweet potato and other plants.

Transcriptomic analysis of differentially expressed genes in an orange-pericarp mutant and wild type in pummelo (Citrus grandis)

BACKGROUND

The external colour of fruit is a crucial quality feature, and the external coloration of most citrus fruits is due to the accumulation of carotenoids. The molecular regulation of carotenoid biosynthesis and accumulation in pericarp is limited due to the lack of mutant. In this work, an orange-pericarp mutant (MT) which showed altered pigmentation in the pericarp was used to identify genes potentially related to the regulation of carotenoid accumulation in the pericarp.

RESULTS

High Performance Liquid Chromatography (HPLC) analysis revealed that the pericarp from MT fruits had a 10.5-fold increase of β-carotene content over that of the Wild Type (WT). Quantitative real-time PCR (qRT-PCR) analysis showed that the expression of all downstream carotenogenic genes was lower in MT than in WT, suggesting that down-regulation is critical for the β-carotene increase in the MT pericarp. RNA-seq analysis of the transcriptome revealed extensive changes in the MT gene expression level, with 168 genes down-regulated and 135 genes up-regulated. Gene ontology (GO) and KEGG pathway analyses indicated seven reliable metabolic pathways are altered in the mutant, including carbon metabolism, starch and sucrose metabolism and biosynthesis of amino acids. The transcription factors and genes corresponding to effected metabolic pathways may involved in the carotenoid regulation was confirmed by the qRT-PCR analysis in the MT pericarp.

CONCLUSIONS

This study has provided a global picture of the gene expression changes in a novel mutant with distinct color in the fruit pericarp of pummelo. Interpretation of differentially expressed genes (DEGs) revealed new insight into the molecular regulation of β-carotene accumulation in the MT pericarp.

MYB and bHLH transcription factor transgenes increase anthocyanin pigmentation in petunia and lisianthus plants, and the petunia phenotypes are strongly enhanced under field conditions

Petunia line Mitchell [MP, Petunia axillaris × (P. axillaris × P. hybrida)] and Eustoma grandiflorum (lisianthus) plants were produced containing a transgene for over-expression of the R2R3-MYB transcription factor [TF; ROSEA1 (ROS1)] that up-regulates flavonoid biosynthesis in Antirrhinum majus. The petunia lines were also crossed with previously produced MP lines containing a Zea mays flavonoid-related basic helix-loop-helix TF transgene (LEAF COLOR, LC), which induces strong vegetative pigmentation when these 35S:LC plants are exposed to high-light levels. 35S:ROS1 lisianthus transgenics had limited changes in anthocyanin pigmentation, specifically, precocious pigmentation of flower petals and increased pigmentation of sepals. RNA transcript levels for two anthocyanin biosynthetic genes, chalcone synthase and anthocyanidin synthase, were increased in the 35S:ROS1 lisianthus petals compared to those of control lines. With MP, the 35S:ROS1 calli showed novel red pigmentation in culture, but this was generally not seen in tissue culture plantlets regenerated from the calli or young plants transferred to soil in the greenhouse. Anthocyanin pigmentation was enhanced in the stems of mature 35S:ROS1 MP plants, but the MP white-flower phenotype was not complemented. Progeny from a 35S:ROS1 × 35S:LC cross had novel pigmentation phenotypes that were not present in either parental line or MP. In particular, there was increased pigment in the petal throat region, and the anthers changed from yellow to purple pigmentation. An outdoor field trial was conducted with the 35S:ROS1, 35S:LC, 35S:ROS1 × 35S:LC and control MP lines. Field conditions rapidly induced intense foliage pigmentation in 35S:LC plants, a phenotype not observed in control MP or equivalent 35S:LC plants maintained in a greenhouse. No difference in plant stature, seed germination, or plant survival was observed between transgenic and control plants.

Scratching the surface: genetic regulation of cuticle assembly in fleshy fruit

The hydrophobic cuticular membrane of land plants performs a number of important roles during fruit development, including protection from a range of abiotic and biotic stresses. The components of the fleshy fruit cuticle are synthesized and secreted from the epidermal cells. While the biosynthetic and transport pathways of the cuticle have been thoroughly investigated for a number of decades, the regulatory mechanisms allowing fine tuning of cuticle deposition are only now beginning to be elucidated. Transcription factors belonging to the APETALA2, homeodomain-leucine zipper IV, and MYB families have been shown to be important regulators of both cuticle biosynthesis and epidermal cell differentiation, highlighting the connection between these processes. The involvement of MADS-box transcription factors demonstrates the link between fruit ripening and cuticle deposition. Epigenetic and post-transcriptional regulatory mechanisms also play a role in the control of cuticle biosynthesis, in addition to phytohormones, such as abscisic acid, that have been shown to stimulate cuticle deposition. These various levels of genetic regulation allow the plant constantly to maintain and adjust the cuticle in response to environmental and developmental cues.

Genome-wide characterization and comparative analysis of R2R3-MYB transcription factors shows the complexity of MYB-associated regulatory networks in Salvia miltiorrhiza

Background

MYB is the largest plant transcription factor gene family playing vital roles in plant growth and development. However, it has not been systematically studied in Salvia miltiorrhiza, an economically important medicinal plant.

Results

Here we report the genome-wide identification and characterization of 110 R2R3-MYBs, the largest subfamily of MYBs in S. miltiorrhiza. The MYB domain and other motifs of SmMYBs are largely conserved with Arabidopsis AtMYBs, whereas the divergence of SmMYBs and AtMYBs also exists, suggesting the conservation and diversity of plant MYBs. SmMYBs and AtMYBs may be classified into 37 subgroups, of which 31 include proteins from S. miltiorrhiza and Arabidopsis, whereas 6 are specific to a species, indicating that the majority of MYBs play conserved roles, while others may exhibit species-specialized functions. SmMYBs are differentially expressed in various tissues of S. miltiorrhiza. The expression profiles are largely consistent with known functions of their Arabidopsis counterparts. The expression of a subset of SmMYBs is regulated by microRNAs, such as miR159, miR319, miR828 and miR858. Based on functional conservation of MYBs in a subgroup, SmMYBs potentially involved in the biosynthesis of bioactive compounds were identified.

Conclusions

A total of 110 R2R3-MYBs were identified and analyzed. The results suggest the complexity of MYB-mediated regulatory networks in S. miltiorrhiza and provide a foundation for understanding the regulatory mechanism of SmMYBs.

Increased accumulation of anthocyanins in Fragaria chiloensis fruits by transient suppression of FcMYB1 gene

Anthocyanins and proanthocyanidins (PAs), flavonoid-derived metabolites with different physiological roles, are produced by plants in a coordinated manner during fruit development by the action of transcription factors (TFs). These regulatory proteins have either an activating or repressing effect over structural genes from the biosynthetic pathway under their control. FaMYB1, a TF belonging to the R2R3-MYB family and isolated from commercial strawberry fruit (Fragaria×ananassa), was reported as a transcriptional repressor and its heterologous over-expression in tobacco flowers suppressed flavonoid-derived compound accumulation. FcMYB1, an ortholog of FaMYB1 isolated from the white Chilean strawberry (Fragaria chiloensis ssp. chiloensis f. chiloensis), showed higher transcript levels in white (F. chiloensis) than in red (F.×ananassa cv. Camarosa) fruits. In order to assess its contribution to the discolored phenotype in F. chiloensis, FcMYB1 was transiently down-regulated in planta using an RNAi-based approach. Quantitative real-time PCR on FcMYB1 down-regulated fruits resulted an up-regulation of anthocyanidin synthase (ANS) and a strong repression of anthocyanidin reductase (ANR) and leucoanthocyanidin reductase (LAR) transcript accumulation. In addition, these fruits showed increased concentrations of anthocyanins and undetectable levels of flavan 3-ols. Altogether, these results indicate a role for FcMYB1 in regulation of the branching-point of the anthocyanin/PA biosynthesis determining the discolored phenotype of the white Chilean strawberry fruit.

ANTHOCYANIN1 from Solanum chilense is more efficient in accumulating anthocyanin metabolites than its Solanum lycopersicum counterpart in association with the ANTHOCYANIN FRUIT phenotype of tomato

Anthocyanins are flavonoid metabolites contributing attractive colors and antioxidant qualities to the human diet. Accordingly, there is a growing interest in developing crops enriched with these compounds. Fruits of the cultivated tomato, Solanum (S.) lycopersicum, do not normally produce high levels of anthocyanins. However, several wild tomato species yield anthocyanin-pigmented fruits, and this trait has been introgressed into the cultivated tomato. Two genes encoding homologous R2R3 MYB transcription factors, termed ANT1 and AN2, were previously genetically implicated in anthocyanin accumulation in tomato fruit peels of the ANTHOCYANIN FRUIT (AFT) genotype originating from S. chilense. Here we compared transgenic tomato plants constitutively over-expressing the S. lycopersicum (35S::ANT1 ( L ) ) or the S. chilense (35S::ANT1 ( C )) allele, and show that each displayed variable levels of purple pigmentation in vegetative as well as reproductive tissues. However, 35S::ANT1 ( C ) was significantly more efficient in producing anthocyanin pigments, attributed to its gene coding-sequence rather than to its transcript levels. These results expand the potential of enhancing anthocyanin levels through engineering coding-sequence polymorphisms in addition to the transcriptional alterations commonly used. In addition, a segregating population obtained from a recombinant genotype revealed that the native ANT1, and not AN2, is fully associated with the AFT phenotype and that ANT1 alone can generate the characteristic phenotype of anthocyanin accumulation in AFT fruits. Our results therefore provide further support to the hypothesis that ANT1 is the gene responsible for anthocyanin accumulation in fruits of the AFT genotype.

Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway

Flavonoids are secondary metabolites involved in several aspects of plant development and defence. They colour fruits and flowers, favouring seed and pollen dispersal, and contribute to plant adaptation to environmental conditions such as cold or UV stresses, and pathogen attacks. Because they affect the quality of flowers (for horticulture), fruits and vegetables, and their derivatives (colour, aroma, stringency, etc.), flavonoids have a high economic value. Furthermore, these compounds possess pharmaceutical properties extremely attractive for human health. Thanks to easily detectable mutant phenotypes, such as modification of petal pigmentation and seeds exhibiting transparent testa, the enzymes involved in the flavonoid biosynthetic pathway have been characterized in several plant species. Conserved features as well as specific differences have been described. Regulation of structural gene expression appears tightly organized in a spatial and temporal way during plant development, and is orchestrated by a ternary complex involving transcription factors from the R2R3-MYB, basic helix-loop-helix (bHLH), and WD40 classes. This MYB-bHLH-WD40 (MBW) complex regulates the genes that encode enzymes specifically involved in the late steps of the pathway leading to the biosynthesis of anthocyanins and condensed tannins. Although several genes encoding transcription factors from these three families have been identified, many gaps remain in our understanding of the regulation of this biosynthetic pathway, especially about the respective roles of bHLH and WD40 proteins. A better knowledge of the regulatory mechanisms of the flavonoid pathway is likely to favour the development of new biotechnological tools for the generation of value-added plants with optimized flavonoid content.

Molecular activities, biosynthesis and evolution of triterpenoid saponins

Saponins are bioactive compounds generally considered to be produced by plants to counteract pathogens and herbivores. Besides their role in plant defense, saponins are of growing interest for drug research as they are active constituents of several folk medicines and provide valuable pharmacological properties. Accordingly, much effort has been put into unraveling the modes of action of saponins, as well as in exploration of their potential for industrial processes and pharmacology. However, the exploitation of saponins for bioengineering crop plants with improved resistances against pests as well as circumvention of laborious and uneconomical extraction procedures for industrial production from plants is hampered by the lack of knowledge and availability of genes in saponin biosynthesis. Although the ability to produce saponins is rather widespread among plants, a complete synthetic pathway has not been elucidated in any single species. Current conceptions consider saponins to be derived from intermediates of the phytosterol pathway, and predominantly enzymes belonging to the multigene families of oxidosqualene cyclases (OSCs), cytochromes P450 (P450s) and family 1 UDP-glycosyltransferases (UGTs) are thought to be involved in their biosynthesis. Formation of unique structural features involves additional biosynthetical enzymes of diverse phylogenetic background. As an example of this, a serine carboxypeptidase-like acyltransferase (SCPL) was recently found to be involved in synthesis of triterpenoid saponins in oats. However, the total number of identified genes in saponin biosynthesis remains low as the complexity and diversity of these multigene families impede gene discovery based on sequence analysis and phylogeny. This review summarizes current knowledge of triterpenoid saponin biosynthesis in plants, molecular activities, evolutionary aspects and perspectives for further gene discovery.

Novel core promoter elements and a cognate transcription factor in the divergent unicellular eukaryote Trichomonas vaginalis

A highly conserved DNA initiator (Inr) element has been the only core promoter element described in the divergent unicellular eukaryote Trichomonas vaginalis, although genome analyses reveal that only ∼75% of protein-coding genes appear to contain an Inr. In search of another core promoter element(s), a nonredundant database containing 5' untranslated regions of expressed T. vaginalis genes was searched for overrepresented DNA motifs and known eukaryotic core promoter elements. In addition to identifying the Inr, two elements that lack sequence similarity to the known protein-coding gene core promoter, motif 3 (M3) and motif 5 (M5), were identified. Mutational and functional analyses demonstrate that both are novel core promoter elements. M3 [(A/G/T)(A/G)C(G/C)G(T/C)T(T/A/G)] resembles a Myb recognition element (MRE) and is bound specifically by a unique protein with a Myb-like DNA binding domain. The M5 element (CCTTT) overlaps the transcription start site and replaces the Inr as an alternative, gene-specific initiator element. Transcription specifically initiates at the second cytosine within M5, in contrast to characteristic initiation by RNA polymerase II at an adenosine. In promoters that combine M3 with either M5 or Inr, transcription initiation is regulated by the M3 motif.

Identification of putative stage-specific grapevine berry biomarkers and omics data integration into networks

The analysis of grapevine (Vitis vinifera) berries at the transcriptomic, proteomic, and metabolomic levels can provide great insight into the molecular events underlying berry development and postharvest drying (withering). However, the large and very different data sets produced by such investigations are difficult to integrate. Here, we report the identification of putative stage-specific biomarkers for berry development and withering and, to our knowledge, the first integrated systems-level study of these processes. Transcriptomic, proteomic, and metabolomic data were integrated using two different strategies, one hypothesis free and the other hypothesis driven. A multistep hypothesis-free approach was applied to data from four developmental stages and three withering intervals, with integration achieved using a hierarchical clustering strategy based on the multivariate bidirectional orthogonal projections to latent structures technique. This identified stage-specific functional networks of linked transcripts, proteins, and metabolites, providing important insights into the key molecular processes that determine the quality characteristics of wine. The hypothesis-driven approach was used to integrate data from three withering intervals, starting with subdata sets of transcripts, proteins, and metabolites. We identified transcripts and proteins that were modulated during withering as well as specific classes of metabolites that accumulated at the same time and used these to select subdata sets of variables. The multivariate bidirectional orthogonal projections to latent structures technique was then used to integrate the subdata sets, identifying variables representing selected molecular processes that take place specifically during berry withering. The impact of this holistic approach on our knowledge of grapevine berry development and withering is discussed.

Comprehensive analysis of expressed sequence tags from the pulp of the red mutant 'Cara Cara' navel orange (Citrus sinensis Osbeck)

Expressed sequence tag (EST) analysis of the pulp of the red-fleshed mutant 'Cara Cara' navel orange provided a starting point for gene discovery and transcriptome survey during citrus fruit maturation. Interpretation of the EST datasets revealed that the mutant pulp transcriptome held a high section of stress responses related genes, such as the type III metallothionein-like gene (6.0%), heat shock protein (2.8%), Cu/Zn superoxide dismutase (0.8%), late embryogenesis abundant protein 5 (0.8%), etc. 133 transcripts were detected to be differentially expressed between the red mutant and its orange-color wild genotype 'Washington' via digital expression analysis. Among them, genes involved in metabolism, defense/stress and signal transduction were statistical overrepresented. Fifteen transcription factors, composed of NAM, ATAF, and CUC transcription factor (NAC); myeloblastosis (MYB); myelocytomatosis (MYC); basic helix-loop-helix (bHLH); basic leucine zipper (bZIP) domain members, were also included. The data reflected the distinct expression profile and the unique regulatory module associated with these two genotypes. Eight differently expressed genes analyzed in digital were validated by quantitative real-time polymerase chain reaction. For structural polymorphism, both simple sequence repeats and single nucleotide polymorphisms (SNP) loci were surveyed; dinucleotide presentation revealed a bias toward AG/GA/TC/CT repeats (52.5%), against GC/CG repeats (0%). SNPs analysis found that transitions (73%) outnumbered transversions (27%). Seventeen potential cultivar-specific and 387 heterozygous SNP loci were detected from 'Cara Cara' and 'Washington' EST pool.

Fruit-surface flavonoid accumulation in tomato is controlled by a SlMYB12-regulated transcriptional network

The cuticle covering plants' aerial surfaces is a unique structure that plays a key role in organ development and protection against diverse stress conditions. A detailed analysis of the tomato colorless-peel y mutant was carried out in the framework of studying the outer surface of reproductive organs. The y mutant peel lacks the yellow flavonoid pigment naringenin chalcone, which has been suggested to influence the characteristics and function of the cuticular layer. Large-scale metabolic and transcript profiling revealed broad effects on both primary and secondary metabolism, related mostly to the biosynthesis of phenylpropanoids, particularly flavonoids. These were not restricted to the fruit or to a specific stage of its development and indicated that the y mutant phenotype is due to a mutation in a regulatory gene. Indeed, expression analyses specified three R2R3-MYB-type transcription factors that were significantly down-regulated in the y mutant fruit peel. One of these, SlMYB12, was mapped to the genomic region on tomato chromosome 1 previously shown to harbor the y mutation. Identification of an additional mutant allele that co-segregates with the colorless-peel trait, specific down-regulation of SlMYB12 and rescue of the y phenotype by overexpression of SlMYB12 on the mutant background, confirmed that a lesion in this regulator underlies the y phenotype. Hence, this work provides novel insight to the study of fleshy fruit cuticular structure and paves the way for the elucidation of the regulatory network that controls flavonoid accumulation in tomato fruit cuticle.