Cloning and molecular analysis of structural genes involved in flavonoid and stilbene biosynthesis in grape (Vitis vinifera L.)

Integrating molecular characterization and metabolites profile revealed CtCHI1's significant role in Carthamus tinctorius L

BACKGROUND

As a traditional Chinese herb, safflower (Carthamus tinctorius L.) is valued for its florets to prevent cardiovascular and cerebrovascular diseases. Basing on previous chemical analysis, the main active compounds are flavonoids in its florets. Although flavonoid biosynthetic pathway has been well-documented in many model species, unique biosynthetic pathway remains to be explored in safflower. Of note, as an important class of transitional enzymes, chalcone isomerase (CHI) has not been characterized in safflower.

RESULTS

According to our previous research, CHIs were identified in a safflower transcriptome library built by our lab. To characterize CHI in safflower, a CHI gene named CtCHI1 was identified. A multiple sequences alignment and phylogenetic tree demonstrate that CtCHI1 shares 92% amino acid identity and close relationship with CHI to Saussurea medusa. Additionally, subcellular localization analysis indicated CtCHI1-GFP fusion protein was mainly in the cell nucleus. Further, we purified CtCHI1 protein from E. coli which can effectively catalyze isomerization of 2',4',4,6'-tetrahydroxychalcone into naringenin in vitro. Via genetic engineer technology, we successfully obtained transgenic tobacco and safflower lines. In transgenic tobacco, overexpression of CtCHI1 significantly inhibited main secondary metabolites accumulation, including quercetin (~ 79.63% for ovx-5 line) and anthocyanins (~ 64.55% for ovx-15 line). As shown in transgenic safflower, overexpression of CtCHI1 resulted in upstream genes CtPAL3 and CtC4H1 increasing dramatically (up to ~ 3.9fold) while Ct4CL3, CtF3H and CtDFR2 were inhibited. Also, comparing the whole metabolomics database by PCA and PLS-DA between transgenic and control group, 788 potential differential metabolites were marked and most of them displayed up-regulated trends. In parallel, some isolated secondary metabolites, such as hydroxysafflor yellow A (HSYA), rutin, kaempferol-3-O-β-rutinoside and dihydrokaempferol, accumulated in transgenic safflower plants.

CONCLUSIONS

In this study, we found that CtCHI1 is an active, functional, catalytic protein. Moreover, CtCHI1 can negatively and competitively regulate anthocyanins and quercetin pathway branches in tobacco. By contrast, CtCHI1 can positively regulate flavonol and chalcone metabolic flow in safflower. This research provides some clues to understand CHI's differential biochemical functional characterization involving in flavonoid pathway. More molecular mechanisms of CHI remain to be explored in the near future.

Stilbene biosynthesis and gene expression in response to methyl jasmonate and continuous light treatment in Vitis vinifera cv. Malvasia del Lazio and Vitis rupestris Du Lot cell cultures

Vitis rupestris is used as rootstock or to obtain hybrids with Vitis vinifera, due to its resistance to certain pathogens. Its resistance mechanisms are poorly understood, while it is known that stilbene neo-synthesis is a central defense strategy in V. vinifera. In the present study, the response to methyl jasmonate (MeJa) and light treatment in terms of stilbene biosynthesis and the expression of genes involved in polyphenol biosynthesis was investigated in V. vinifera and V. rupestris cells. The two species exhibited a similar constitutive stilbene content [2.50-2.80 mg g^-1 dry weight (DW)], which greatly increased in response to elicitation (8.97-11.90 mg g^-1 DW). In V. vinifera, continuous light treatment amplified the effect of MeJa, with a stilbene production that had never previously been obtained (26.49 mg g^-1 DW). By contrast, it suppressed the effect of MeJa in V. rupestris. Gene expression was consistent with stilbene production in V. vinifera, whereas discrepancies were recorded in V. rupestris that could be explained by the synthesis of stilbenes that had never before been analyzed in this species.

Transcriptomics of the grape berry shrivel ripening disorder

The lower expression at veraison of several ripening master regulators "switch genes" can play a central role in the induction of the berry shrivel ripening physiological disorder in grapevine. Berry shrivel (BS) is a ripening physiological disorder affecting grape berry with visible symptoms appearing after veraison. Berry shrivel leads to shrinking berries with a reduced weight and a lower content of sugars and anthocyanins. In this study, for the first time a transcriptomic analysis coupled with selected metabolites quantification was undertaken to understand the metabolic modifications induced by the disorder. Different stages of berry development were considered including pre- and symptomatic berries. No metabolic alterations in the berry transcriptome and in the metabolite content was observed in pre-symptomatic and pre-veraison samples. Interestingly, at veraison, with still not visible symptoms appearing on the berry, a subset of genes, called switch genes previously suggested as master regulators of the ripening onset in grape berries, were strongly lower expressed in BS. Later during the ripening phase and with visible symptoms of the disorder, more than 3000 genes were differentially expressed. The genes up-regulated were related to hormone biosynthesis, response to stress and the phenylpropanoid pathway, while the genes down-regulated during ripening belonged mainly to the flavonoid pathway, and the sugar metabolism. In agreement, BS berries showed lower content of sugars and anthocyanins from the onset of veraison onward, while the amount of acids was not significantly affected. In conclusion, these results highlight a pivotal role of the switch genes in grapevine ripening, as well as their possible contribution to induce the ripening disorder berry shrivel, although it remains unclear whether this is part of the cause or consequences of the BS disorder.

Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development

Transcriptomics has been widely applied to study grape berry development. With few exceptions, transcriptomic studies in grape are performed using the available genome sequence, PN40024, as reference. However, differences in gene content among grape accessions, which contribute to phenotypic differences among cultivars, suggest that a single reference genome does not represent the species' entire gene space. Though whole genome assembly and annotation can reveal the relatively unique or "private" gene space of any particular cultivar, transcriptome reconstruction is a more rapid, less costly, and less computationally intensive strategy to accomplish the same goal. In this study, we used single molecule-real time sequencing (SMRT) to sequence full-length cDNA (Iso-Seq) and reconstruct the transcriptome of Cabernet Sauvignon berries during berry ripening. In addition, short reads from ripening berries were used to error-correct low-expression isoforms and to profile isoform expression. By comparing the annotated gene space of Cabernet Sauvignon to other grape cultivars, we demonstrate that the transcriptome reference built with Iso-Seq data represents most of the expressed genes in the grape berries and includes 1,501 cultivar-specific genes. Iso-Seq produced transcriptome profiles similar to those obtained after mapping on a complete genome reference. Together, these results justify the application of Iso-Seq to identify cultivar-specific genes and build a comprehensive reference for transcriptional profiling that circumvents the necessity of a genome reference with its associated costs and computational weight.

Comparative Transcriptome Analysis of the Skin-Specific Accumulation of Anthocyanins in Black Peanut ( Arachis hypogaea L.)

As an oil crop with good taste and profuse nutrition, peanut ( Arachis hypogaea L.) is grown worldwide, mainly for edible seeds. Black peanuts attract more attention for their appealing color and health-promoting anthocyanins. Here, two cyanidin-based anthocyanins and four quercetin-based flavonols were separated and identified from skins of two black cultivars (Zi Yu and Zi Guan) by HPLC-ESI-Q-TOF-MS. To study the anthocyanin accumulation, libraries constructed from the mRNA of skins of Zi Yu and white cultivar (Bai Yu) were sequenced, and 4042 differentially expressed genes were identified. Gene ontology and KEGG pathway analysis underlined the importance of the high expression of flavonoid biosynthetic and regulatory genes in seed skin of Zi Yu. Furthermore, expression profiles of these genes were analyzed carefully in four representative peanut cultivars. Altogether, these results strongly indicate that the up-regulation of transcriptional activators (AhMYB1, AhMYB2, and AhTT8) accounts for the skin-specific accumulation of anthocyanins in black peanut.

Chalcone Isomerase a Key Enzyme for Anthocyanin Biosynthesis in Ophiorrhiza japonica

Anthocyanins are distributed ubiquitously to terrestrial plants and chalcone isomerase (CHI) catalyzes the stereospecific isomerization of chalcones - a committed step in the anthocyanin biosynthesis pathway. In this study, one gene encoding CHI was isolated from Ophiorrhiza japonica and designated as OjCHI. Multiple sequence alignments and phylogenetic analysis revealed that OjCHI had the conserved CHI active site residues and was classified into type I CHI group. In order to better understand the mechanisms of anthocyanin synthesis in O. japonica, integrative analysis between metabolites and OjCHI expression was conducted. The results showed OjCHI expression matched the accumulation patterns of anthocyanins not only in different tissues but also during the flower developmental stages, suggesting the potential roles of OjCHI in the biosynthesis of anthocyanin. Then biochemical analysis indicated that recombinant OjCHI protein exhibited a typical type I CHI activity which catalyzed the production of naringenin from naringenin chalcone. Moreover, expressing OjCHI in Arabidopsis tt5 mutant restored the anthocyanins and flavonols phenotype of hypocotyl, cotyledon and seed coat, indicating its function as a chalcone isomerase in vivo. In summary, our findings reveal the in vitro as well as in vivo functions of OjCHI and provide a resource to understand the mechanism of anthocyanin biosynthesis in O. japonica.

Two R2R3-MYB proteins are broad repressors of flavonoid and phenylpropanoid metabolism in poplar

The phenylpropanoid pathway leads to the production of many important plant secondary metabolites including lignin, chlorogenic acids, flavonoids, and phenolic glycosides. Early studies have demonstrated that flavonoid biosynthesis is transcriptionally regulated, often by a MYB, bHLH, and WDR transcription factor complex. In poplar, several R2R3 MYB transcription factors are known to be involved in flavonoid biosynthesis. Previous work determined that poplar MYB134 and MYB115 are major activators of the proanthocyanidin pathway, and also induce the expression of repressor-like MYB transcription factors. Here we characterize two new repressor MYBs, poplar MYB165 and MYB194, paralogs which comprise a subgroup of R2R3-MYBs distinct from previously reported poplar repressors. Both MYB165 and MYB194 repressed the activation of flavonoid promoters by MYB134 in transient activation assays, and both interacted with a co-expressed bHLH transcription factor, bHLH131, in yeast two-hybrid assays. Overexpression of MYB165 and MYB194 in hybrid poplar resulted in greatly reduced accumulation of several phenylpropanoids including anthocyanins, proanthocyanidins, phenolic glycosides, and hydroxycinnamic acid esters. Transcriptome analysis of MYB165- and MYB194-overexpressing poplars confirmed repression of many phenylpropanoid enzyme genes. In addition, other MYB genes as well as several shikimate pathway enzyme genes were downregulated by MYB165-overexpression. By contrast, leaf aromatic amino acid concentrations were greater in MYB165-overexpressing poplars. Our findings indicate that MYB165 is a major repressor of the flavonoid and phenylpropanoid pathway in poplar, and may also affect the shikimate pathway. The coordinated action of repressor and activator MYBs could be important for the fine tuning of proanthocyanidin biosynthesis during development or following stress.

Resveratrol: from enhanced biosynthesis and bioavailability to multitargeting chronic diseases

Resveratrol, a phytoalexin with a wide range of pharmacological properties is synthesised by plants in response to stress, injury, infection or UV radiations. As it is a secondary metabolite with many health promoting properties, various methods employing microorganisms and genetic manipulation of different synthetic enzymes, have been comprehensively studied to increase its production. Its rapid metabolism and low bioavailability have been addressed by the use of bio enhancers and nano-formulations. This flavonoid is extensively researched due to its pharmacological properties such as anti-oxidative, anti-inflammatory and immuno-modulating effects. Knowledge of these properties of resveratrol has led to elaborate studies on its effect on diabetes, neurodegenerative diseases, cancer, ageing, obesity and cardiovascular diseases. At molecular level it targets sirtuin, adenosine monophosphate kinase, nuclear Factor-κB, inflammatory cytokines, anti-oxidant enzymes along with cellular processes such as angiogenesis, apoptosis, mitochondrial biogenesis, gluconeogenesis and lipid metabolism. This review discusses the properties of resveratrol and the different approaches of addressing the unfavourable synthesis and pharmacokinetics of this stilbene. Pre-clinical evaluations of resveratrol on diabetes mellitus, cardiovascular and neurological diseases are elaborately discussed and the underlying pathways involved in its therapeutic activity have been given paramount importance. Following the pre-clinical studies, clinical trials on the same reveal the efficacy of resveratrol in the effective management of these diseases. This review provides an intricate insight on resveratrol's significance from a dietary component to a therapeutic agent.

Neuroprotective Mechanisms of Resveratrol in Alzheimer's Disease: Role of SIRT1

Alzheimer's disease (AD) is a progressive and neurodegenerative disorder of the cortex and hippocampus, which eventually leads to cognitive impairment. Although the etiology of AD remains unclear, the presence of β-amyloid (Aβ) peptides in these learning and memory regions is a hallmark of AD. Therefore, the inhibition of Aβ peptide aggregation has been considered the primary therapeutic strategy for AD treatment. Many studies have shown that resveratrol has antioxidant, anti-inflammatory, and neuroprotective properties and can decrease the toxicity and aggregation of Aβ peptides in the hippocampus of AD patients, promote neurogenesis, and prevent hippocampal damage. In addition, the antioxidant activity of resveratrol plays an important role in neuronal differentiation through the activation of silent information regulator-1 (SIRT1). SIRT1 plays a vital role in the growth and differentiation of neurons and prevents the apoptotic death of these neurons by deacetylating and repressing p53 activity; however, the exact mechanisms remain unclear. Resveratrol also has anti-inflammatory effects as it suppresses M1 microglia activation, which is involved in the initiation of neurodegeneration, and promotes Th2 responses by increasing anti-inflammatory cytokines and SIRT1 expression. This review will focus on the antioxidant and anti-inflammatory neuroprotective effects of resveratrol, specifically on its role in SIRT1 and the association with AD pathophysiology.

Simulation of different three-dimensional polymer models of interphase chromosomes compared to experiments-an evaluation and review framework of the 3D genome organization

Despite all the efforts the three-dimensional higher-order architecture and dynamics in the cell nucleus are still debated. The regulation of genes, their transcription, replication, as well as differentiation in Eukarya is, however, closely connected to this architecture and dynamics. Here, an evaluation and review framework is setup to investigate the folding of a 30 nm chromatin fibre into chromosome territories by comparing computer simulations of two different chromatin topologies to experiments: The Multi-Loop-Subcompartment (MLS) model, in which small loops form rosettes connected by chromatin linkers, and the Random-Walk/Giant-Loop (RW/GL) model, in which large loops are attached to a flexible non-protein backbone, were simulated for various loop, rosette, and linker sizes. The 30 nm chromatin fibre was modelled as a polymer chain with stretching, bending, and excluded volume interactions. A spherical boundary potential simulated the confinement by other chromosomes and the nuclear envelope. Monte Carlo and Brownian Dynamics methods were applied to generate chain configurations at thermodynamic equilibrium. Both the MLS and the RW/GL models form chromosome territories, with different morphologies: The MLS rosettes form distinct subchromosomal domains, compatible in size as those from light microscopic observations. In contrast, the big RW/GL loops lead to a more homogeneous chromatin distribution. Only the MLS model agrees with the low overlap of chromosomes, their arms, and subchromosomal domains found experimentally. A review of experimental spatial distance measurements between genomic markers labelled by FISH as a function of their genomic separation from different publications and comparison to simulated spatial distances also favours an MLS-like model with loops and linkers of 63 to 126 kbp. The chromatin folding topology also reduces the apparent persistence length of the chromatin fibre to a value significantly lower than the free solution persistence length, explaining the low persistence lengths found various experiments. The predicted large spaces between the chromatin fibres allow typically sized biological molecules to reach nearly every location in the nucleus by moderately obstructed diffusion and disagrees with the much simplified assumption that defined channels between territories for molecular transport as in the Interchromosomal Domain (ICD) hypothesis exist. All this is also in agreement with recent selective high-resolution chromosome interaction capture (T2C) experiments, the scaling behaviour of the DNA sequence, the dynamics of the chromatin fibre, the nuclear diffusion of molecules, as well as other experiments. In summary, this polymer simulation framework compared to experimental data clearly favours only a quasi-chromatin fibre forming a stable multi-loop aggregate/rosette like genome organization and dynamics whose local topology is tightly connected to the global morphology and dynamics of the cell nucleus.

Grapevine fanleaf virus affects grape (Vitis vinifera) berry anthocyanin content via the transcriptional regulation of anthocyanin biosynthetic genes

Grapevine fanleaf virus (GFLV) causes grapevine fanleaf degeneration, one of the oldest known viral diseases of grapevines. The virus has been found in all winegrowing regions around the world. In the seasons 2011-12 a comparison between field grown GFLV-infected and healthy grapevines was conducted for the cultivars Schioppettino in North-Eastern Italy and Refošk in South-Western Slovenia. Our research showed that GFLV infection caused a drop of the yield due to reduction of both cluster weight and berry weight. Besides the yield, the berry composition was also affected; in detail, anthocyanin concentration increased in both varieties but significantly only in the case of Schioppettino. Upregulation of the F3'5'H gene and downregulation of F3'H gene in the berries of GFLV infected vines compared with the ones of healthy control vines resulted in modified proportions between di- and tri- hydroxylated or methylated derivatives of anthocyanins. The F3H1 gene was identified to be the most strongly regulated gene of the flavonoid biosynthetic pathway by GFLV infection, indicating its important role in increasing anthocyanin concentration in grapes of GFLV infected vines as compared with healthy controls.

Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume)

The red-skinned fruit of Japanese apricot (Prunus mume Sieb. et Zucc) appeals to customers due to its eye-catching pigmentation, while the mechanism related to its colour formation is still unclear. In this study, genome re-sequencing of six Japanese apricot cultivars was carried out with approximately 92.2 Gb of clean bases using next-generation sequencing. A total of 32,004 unigenes were assembled with an average of 83.1% coverage rate relative to reference genome. A wide range of genetic variation was detected, including 7,387,057 single nucleotide polymorphisms, 456,222 insertions or deletions and 129,061 structural variations in all genomes. Comparative sequencing data revealed that 13 candidate genes were involved in biosynthesis of anthocyanin. Significantly higher expression patterns were observed in genes encoding three anthocyanin synthesis structural genes (4CL, F3H and UFGT), five transcription factors (MYB–bHLH–WD40 complexes and NAC) and five anthocyanin accumulation related genes (GST1, RT1, UGT85A2, ABC and MATE transporters) in red-skinned than in green-skinned Japanese apricots using reverse transcription-quantitative polymerase chain reaction. Eight main kinds of anthocyanin s were detected by UPLC/MS, and cyanidin 3-glucoside was identified as the major anthocyanin (124.2 mg/kg) in red-skinned cultivars. The activity of UDP-glucose flavonoid-3-O-glycosyltransferase enzyme determined by UPLC was significantly higher in all red-skinned cultivars, suggesting that it is the potential vital regulatory gene for biosynthesis of anthocyanin in Japanese apricot.

Molecular Cloning and Functional Characterization of a Dihydroflavonol 4-Reductase from Vitis bellula

Vitis bellula is a new grape crop in southern China. Berries of this species are rich in antioxidative anthocyanins and proanthocyanidins. This study reports cloning and functional characterization of a cDNA encoding a V. bellula dihydroflavonol reductase (VbDFR) involved in the biosynthesis of anthocyanins and proanthocyanidins. A cDNA including 1014 bp was cloned from young leaves and its open reading frame (ORF) was deduced encoding 337 amino acids, highly similar to V. vinifera DFR (VvDFR). Green florescence protein fusion and confocal microscopy analysis determined the cytosolic localization of VbDFR in plant cells. A soluble recombinant VbDFR was induced and purified from E. coli for enzyme assay. In the presence of NADPH, the recombinant enzyme catalyzed dihydrokaempferol (DHK) and dihydroquercetin (DHQ) to their corresponding leucoanthocyanidins. The VbDFR cDNA was introduced into tobacco plants via Agrobacterium-mediated transformation. The overexpression of VbDFR increased anthocyanin production in flowers. Anthocyanin hydrolysis and chromatographic analysis revealed that transgenic flowers produced pelargonidin and delphinidin, which were not detected in control flowers. These data demonstrated that the overexpression of VbDFR produced new tobacco anthocyanidins. In summary, all data demonstrate that VbDFR is a useful gene to provide three types of substrates for metabolic engineering of anthocyanins and proanthocyanidins in grape crops and other crops.

The ripening disorder berry shrivel affects anthocyanin biosynthesis and sugar metabolism in Zweigelt grape berries

MAIN CONCLUSION

Timescale analyses suggest the berry shrivel (BS) disorder is induced before veraison with strong effects on anthocyanin biosynthesis, and minor effects on sugar transport and metabolism. Berry shrivel (BS)-affected grapes have low sugar contents, high acidity, less anthocyanins and flaccid berries. To date no pathogenic causes are known, and studies to elucidate the molecular basis leading to symptom induction and development are limited. Here we present a study on pre-symptomatic as well as symptomatic BS berries to characterize early metabolic changes, with focus on anthocyanin biosynthesis and sugars metabolism. Healthy and BS berries from six sampling time points were used (BBCH79-BBCH89). Our objectives are (1) to search for the beginning of BS-related physiological processes; (2) to search for key enzymes and sugar transporters involved in BS induction and development and (3) to understand the consequences on polyphenol biosynthesis. We employed high performance anion exchange chromatography coupled with pulsed amperometric detection (HPAEC-PAD) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology for sugar and polyphenol analyses, respectively. Additionally we conducted expression analyses (qPCR) of key genes and enzymatic activity assays. Our results show that BS-related processes start before veraison, as determined by slightly reduced hexose contents and reduced expression levels of a vacuolar invertase (VviGIN1), two monosaccharide transporters (VviTMT2, VviTMT3) and the anthocyanin biosynthesis (VviUFGT, VviMYBA1/2) genes. Lower amounts of delphinidin and cyanidin glycosidic forms were determined, while caftaric acid, quercetin-3-O-glucuronide and (+)-catechin were increased in BS berries. Although not all results were conclusive, especially for the sugar metabolism, our data provide important knowledge to improve the understanding of the highly complex berry shrivel ripening disorder.

Anthocyanin Management in Fruits by Fertilization

Anthocyanins are water-soluble vacuolar plant pigments that are mainly synthesized in epidermal layers and the flesh of fruits such as apples, cherries, grapes, and other berries. Because of their attractive red to purple coloration and their health-promoting potential, anthocyanins are significant determinants for the quality and market value of fruits and fruit-derived products. In crops, anthocyanin accumulation in leaves can be caused by nutrient deficiency which is usually ascribed to insufficient nitrogen or phosphorus fertilization. However, it is a little-known fact that the plant's nutrient status also impacts anthocyanin synthesis in fruits. Hence, strategic nutrient supply can be a powerful tool to modify the anthocyanin content and consequently the quality and market value of important agricultural commodities. Here we summarize the current knowledge of the influence of plant nutrients on anthocyanin synthesis in fruits of major global market value and discuss the underlying cellular processes that integrate nutrient signaling with fruit anthocyanin formation. It is highlighted that fertilization that is finely tuned in amount and timing has the potential to positively influence the fruit quality by regulating anthocyanin levels. We outline new approaches to enrich plant based foods with health-promoting anthocyanins.

Identification of chalcone isomerase in the basal land plants reveals an ancient evolution of enzymatic cyclization activity for synthesis of flavonoids

Flavonoids ubiquitously distribute to the terrestrial plants and chalcone isomerase (CHI)-catalyzed intramolecular and stereospecific cyclization of chalcones is a committed step in the production of flavonoids. However, so far the bona fide CHIs are found only in vascular plants, and their origin and evolution remains elusive. We conducted transcriptomic and/or genomic sequence search, subsequent phylogenetic analysis, and detailed biochemical and genetic characterization to explore the potential existence of CHI proteins in the basal bryophyte liverwort species and the lycophyte Selaginella moellendorffii. We found that both liverwort and Selaginella species possess canonical CHI-fold proteins that cluster with their corresponding higher plant counterparts. Among them, some members exhibited bona fide CHI activity, which catalyze stereospecific cyclization of both 6'-hydroxychalcone and 6'-deoxychalcone, yielding corresponding 5-hydroxy and 5-deoxyflavanones, resembling the typical type II CHIs currently known to be 'specific' for legume plants. Expressing those primitive bona fide CHIs in the Arabidopsis chi mutant restores the seed coat transparent testa phenotype and the accumulation of flavonoids. These findings, in contrast to our current understanding of the evolution of enzymatic CHIs, suggest that emergence of the bona fide type II CHIs is an ancient evolution event that occurred before the divergence of liverwort lineages.

Vanillylacetone up-regulates anthocyanin accumulation and expression of anthocyanin biosynthetic genes by inducing endogenous abscisic acid in grapevine tissues

We investigated the effect of vanillylacetone (VA) on anthocyanin accumulation with aim of improving grape berry coloration. Spraying Vitis vinifera cv. Muscat Bailey A berries with VA at veraison increased sugar/acid ratio, an indicator of maturation and total anthocyanin accumulation. To elucidate the molecular mechanism underlying the effect of VA on anthocyanin accumulation, in vitro VA treatment of a grapevine cell culture was carried out. Endogenous abscisic acid (ABA) content was higher in the VA-treated cell cultures than in control at 3h after treatment. Consistent with this, the relative expression levels of anthocyanin-synthesis-related genes, including DFR, LDOX, MybA1 and UFGT, in VA-treated cell cultures were much higher than those in control, and high total anthocyanin accumulation was noted in the VA-treated cell cultures as well. These results suggest that VA up-regulates the expression of genes leading to anthocyanin accumulation by inducing endogenous ABA. In addition, VA increased total anthocyanin content in a dose-dependent manner. Although VA treatment in combination with exogenous ABA did not exhibit any synergistic effect, treatment with VA alone showed an equivalent effect to that with exogenous ABA alone on total anthocyanin accumulation. These findings point to the possibility of using VA for improving grape berry coloration.

Expression patterns and promoter characteristics of the Vitis quinquangularis VqSTS36 gene involved in abiotic and biotic stress response

Resveratrol is a stilbene compound that is synthesized by plants in response to biotic stress and has been linked to health benefits associated with the consumption of certain foods and food products, such as grapes and wine. The final step in the biosynthesis of resveratrol is catalyzed by the enzyme stilbene synthase (STS). Here, we assessed the expression of two STS genes (VqSTS36 and VpSTS36) from the wild grape species Vitis quinquangularis (accession 'Shang-24'; powdery mildew (PM) resistant) and Vitis pseudoreticulata (accession 'Hunan-1'; PM susceptible) following infection by Uncinula necator (Schw.) Burr, the causal agent of PM disease. Some correlation was observed between the relative levels of STS36 transcript and disease resistance. We also cloned the 5' upstream sequence of both VpSTS36 and VqSTS36 and generated a series of 5' VqSTS36 promoter deletions fused to the GUS reporter gene in order to analyze expression in response to wounding, the application of exogenous stress-associated hormones, and biotic stress in tobacco leaves. The promoter was shown to be induced by the hormone salicylic acid (SA), inoculation with the fungal pathogen Erysiphe cichoracearum, and by wounding. These results suggest that VqSTS36 is regulated by biotic stresses and that it plays an important role in mediating disease resistance in grape.

Iron deficiency stimulates anthocyanin accumulation in grapevine apical leaves

Iron chlorosis is a diffuse disorder affecting Mediterranean vineyards. Beside the commonly described symptom of chlorophyll decrease, an apex reddening was recently observed. Secondary metabolites, such as anthocyanins, are often synthetized to cope with stresses in plants. The present work aimed to evaluate grapevine responses to iron deficiency, in terms of anthocyanin metabolism (reflectance spectrum, total anthocyanin content, HPLC profile and gene expression) in apical leaves of Cabernet sauvignon and Sangiovese grown in hydroponic conditions. Iron supply interruption produced after one month an increasing of anthocyanin content associated to a more stable profile in both cultivars. In Cabernet sauvignon, the higher red pigment accumulation was associated to a lower intensity of chlorotic symptoms, while in Sangiovese, despite the activation of the metabolism, the lower anthocyanin accumulation was associated to a stronger decrease in chlorophyll concentration. Gene expression data showed a significant increase of anthocyanin biosynthesis. The effects on the expression of structural and transcription factor genes of phenylpropanoid pathway were cultivar dependent. F3H, F3'H, F3'5'H and LDOX genes, in Cabernet sauvignon, and AOMT1 and AOMT genes, in Sangiovese, were positively affected by the treatment in response to iron deficiency. All data support the hypothesis of an anthocyanin biosynthesis stimulation rather than a decreased degradation of them due to iron chlorosis.

Identification of Biomarkers for Defense Response to Plasmopara viticola in a Resistant Grape Variety

Downy mildew (Plasmopara viticola) is one of the most destructive diseases of the cultivated species Vitis vinifera. The use of resistant varieties, originally derived from backcrosses of North American Vitis spp., is a promising solution to reduce disease damage in the vineyards. To shed light on the type and the timing of pathogen-triggered resistance, this work aimed at discovering biomarkers for the defense response in the resistant variety Bianca, using leaf discs after inoculation with a suspension of P. viticola. We investigated primary and secondary metabolism at 12, 24, 48, and 96 h post-inoculation (hpi). We used methods of identification and quantification for lipids (LC-MS/MS), phenols (LC-MS/MS), primary compounds (GC-MS), and semi-quantification for volatile compounds (GC-MS). We were able to identify and quantify or semi-quantify 176 metabolites, among which 53 were modulated in response to pathogen infection. The earliest changes occurred in primary metabolism at 24-48 hpi and involved lipid compounds, specifically unsaturated fatty acid and ceramide; amino acids, in particular proline; and some acids and sugars. At 48 hpi, we also found changes in volatile compounds and accumulation of benzaldehyde, a promoter of salicylic acid-mediated defense. Secondary metabolism was strongly induced only at later stages. The classes of compounds that increased at 96 hpi included phenylpropanoids, flavonols, stilbenes, and stilbenoids. Among stilbenoids we found an accumulation of ampelopsin H + vaticanol C, pallidol, ampelopsin D + quadrangularin A, Z-miyabenol C, and α-viniferin in inoculated samples. Some of these compounds are known as phytoalexins, while others are novel biomarkers for the defense response in Bianca. This work highlighted some important aspects of the host response to P. viticola in a commercial variety under controlled conditions, providing biomarkers for a better understanding of the mechanism of plant defense and a potential application in field studies of resistant varieties.

CRISPR/Cas9-mediated mutagenesis of the dihydroflavonol-4-reductase-B (DFR-B) locus in the Japanese morning glory Ipomoea (Pharbitis) nil

CRISPR/Cas9 technology is a versatile tool for targeted mutagenesis in many organisms, including plants. However, this technique has not been applied to the Japanese morning glory (Ipomoea [Pharbitis] nil), a traditional garden plant chosen for the National BioResource Project in Japan. We selected dihydroflavonol-4-reductase-B (DFR-B) of I. nil, encoding an anthocyanin biosynthesis enzyme, as the target gene, and changes in the stem colour were observed during the early stages of plant tissue culture by Rhizobium [Agrobacterium]-mediated transformation. Twenty-four of the 32 (75%) transgenic plants bore anthocyanin-less white flowers with bi-allelic mutations at the Cas9 cleavage site in DFR-B, exhibiting a single base insertion or deletions of more than two bases. Thus, these results demonstrate that CRISPR/Cas9 technology enables the exploration of gene functions in this model horticultural plant. To our knowledge, this report is the first concerning flower colour changes in higher plants using CRISPR/Cas9 technology.

A Study on the Expression of Genes Involved in Carotenoids and Anthocyanins During Ripening in Fruit Peel of Green, Yellow, and Red Colored Mango Cultivars

Mango (Mangiferaindica L.) fruits are generally classified based on peel color into green, yellow, and red types. Mango peel turns from green to yellow or red or retain green colors during ripening. The carotenoids and anthocyanins are the important pigments responsible for the colors of fruits. In the present study, peels of different colored cultivars at three ripening stages were characterized for pigments, colors, and gene expression analysis. The yellow colored cultivar "Arka Anmol" showed higher carotenoid content, wherein β-carotene followed by violaxanthin were the major carotenoid compounds that increased during ripening. The red colored cultivars were characterized with higher anthocyanins with cyanidin-3-O-monoglucosides and peonidin-3-O-glucosides as the major anthocyanins. The gene expression analysis by qRT-PCR showed the higher expression of carotenoid biosynthetic genes viz. lycopene-β-cyclase and violaxanthin-de-epoxidase in yellow colored cv. Arka Anmol, and the expression was found to increase during ripening. However, in red colored cv. "Janardhan Pasand," there is increased regulation of all anthocyanin biosynthetic genes including transcription factors MYB and basic helix loop. This indicated the regulation of the anthocyanins by these genes in red mango peel. The results showed that the accumulation pattern of particular pigments and higher expression of specific biosynthetic genes in mango peel impart different colors.

Light-induced Variation in Phenolic Compounds in Cabernet Sauvignon Grapes (Vitis vinifera L.) Involves Extensive Transcriptome Reprogramming of Biosynthetic Enzymes, Transcription Factors, and Phytohormonal Regulators

Light environments have long been known to influence grape (Vitis vinifera L.) berry development and biosynthesis of phenolic compounds, and ultimately affect wine quality. Here, the accumulation and compositional changes of hydroxycinnamic acids (HCAs) and flavonoids, as well as global gene expression were analyzed in Cabernet Sauvignon grape berries under sunlight exposure treatments at different phenological stages. Sunlight exposure did not consistently affect the accumulation of berry skin flavan-3-ol or anthocyanin among different seasons due to climatic variations, but increased HCA content significantly at véraison and harvest, and enhanced flavonol accumulation dramatically with its timing and severity degree trend. As in sunlight exposed berries, a highly significant correlation was observed between the expression of genes coding phenylalanine ammonia-lyase, 4-coumarate: CoA ligase, flavanone 3-hydroxylase and flavonol synthase family members and corresponding metabolite accumulation in the phenolic biosynthesis pathway, which may positively or negatively be regulated by MYB, bHLH, WRKY, AP2/EREBP, C2C2, NAC, and C2H2 transcription factors (TFs). Furthermore, some candidate genes required for auxin, ethylene and abscisic acid signal transductions were also identified which are probably involved in berry development and flavonoid biosynthesis in response to enhanced sunlight irradiation. Taken together, this study provides a valuable overview of the light-induced phenolic metabolism and transcriptome changes, especially the dynamic responses of TFs and signaling components of phytohormones, and contributes to the further understanding of sunlight-responsive phenolic biosynthesis regulation in grape berries.

Isolation of CHS Gene from Brunfelsia acuminata Flowers and Its Regulation in Anthocyanin Biosysthesis

Chalcone synthase gene (BaCHS) from Brunfelsia acuminata flowers was isolated using RT-PCR and RACE. The coding region of the gene is 1425-bp with an open reading frame of 1170-bp, 73-bp 5'UTR, and 172-bp 3'UTR. Its deduced protein does not have a signal peptide but does contain a cond_enzyme superfamily domain, and consists of 389 amino acids with a predicted molecular mass of 42,699 Da and a pI of 6.57. The deduced amino acid sequence of BaCHS shares 90%, 88%, 85%, 84% and 79% identity with CHS from Petunia hybrida, Nicotiana tabacum, Solanum lycopersicum, Capsicum annuum and Camellia sinensis, respectively. The striking color change from dark purple to light purple and ultimately lead to pure white resulted from a decline in anthocyanin content of the petals and was preceded by a decrease in the expression of BaCHS. Its gene expression was positively correlated with the contents of anthocyanin (p ≤ 0.01).

Transcriptome analysis of genes involved in anthocyanins biosynthesis and transport in berries of black and white spine grapes (Vitis davidii)

Background

The color of berry skin is an important economic trait for grape and is essentially determined by the components and content of anthocyanins. The fruit color of Chinese wild grapes is generally black, and the profile of anthocyanins in Chinese wild grapes is significantly different from that of Vitis vinifera. However, V. davidii is the only species that possesses white berry varieties among Chinese wild grape species. Thus, we performed a transcriptomic analysis to compare the difference of transcriptional level in black and white V. davidii, in order to find some key genes that are related to anthocyanins accumulation in V. davidii.

Results

The results of anthocyanins detection revealed that 3,5-O-diglucoside anthocyanins is the predominant anthocyanins in V. davidii. It showed obvious differences from V. vinifera in the profile of the composition of anthocyanins. The transcriptome sequencing by Illumina mRNA-Seq technology generated an average of 57 million 100-base pair clean reads from each sample. Differential gene expression analysis revealed thousands of differential expression genes (DEGs) in the pairwise comparison of different fruit developmental stages between and within black and white V. davidii. After the analysis of functional category enrichment and differential expression patterns of DEGs, 46 genes were selected as the candidate genes. Some genes have been reported as being related to anthocyanins accumulation, and some genes were newly found in our study as probably being related to anthocyanins accumulation. We inferred that 3AT (VIT_03s0017g00870) played an important role in anthocyanin acylation, GST4 (VIT_04s0079g00690) and AM2 (VIT_16s0050g00910) played important roles in anthocyanins transport in V. davidii. The expression of some selected DEGs was further confirmed by quantitative real-time PCR (qRT-PCR).

Conclusions

The present study investigated the transcriptomic profiles of berry skin from black and white spine grapes at three fruit developmental stages by Illumina mRNA-Seq technology. It revealed the variety specificity of anthocyanins accumulation in V. davidi at the transcriptional level. The data reported here will provide a valuable resource for understanding anthocyanins accumulation in grapes, especially in V. davidii.

Electronic supplementary material

The online version of this article (doi:10.1186/s41065-016-0021-1) contains supplementary material, which is available to authorized users.

Variation in Key Flavonoid Biosynthetic Enzymes and Phytochemicals in 'Rio Red' Grapefruit (Citrus paradisi Macf.) during Fruit Development

In the current study, the phytochemical contents and expression of genes involved in flavonoid biosynthesis in Rio Red grapefruit were studied at different developmental and maturity stages for the first time. Grapefruit were harvested in June, August, November, January, and April and analyzed for the levels of carotenoids, vitamin C, limonoids, flavonoids, and furocoumarins by HPLC. In addition, genes encoding for phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), and 1,2-rhamnosyltransferase (2RT) were isolated, and their expression in grapefruit juice vesicles was studied. Fruit maturity had significant influence on the expression of the genes, with PAL, CHS, and CHI having higher expression in immature fruits (June), whereas 2RT expression was higher in mature fruits (November and January). The levels of flavonoids (except naringin and poncirin), vitamin C, and furocoumarins gradually decreased from June to April. Furthermore, limonin levels sharply decreased in January. Lycopene decreased whereas β-carotene gradually increased with fruit maturity. Naringin did not exactly follow the pattern of 2RT or of PAL, CHS, and CHI expression, indicating that the four genes may have complementary effects on the level of naringin. Nevertheless, of the marketable fruit stages, early-season grapefruits harvested in November contained more beneficial phytochemicals as compared to mid- and late-season fruits harvested in January and April, respectively.

Transcriptome Analysis Reveals the Genetic Basis of the Resveratrol Biosynthesis Pathway in an Endophytic Fungus (Alternaria sp. MG1) Isolated from Vitis vinifera

Alternaria sp. MG1, an endophytic fungus previously isolated from Merlot grape, produces resveratrol from glucose, showing similar metabolic flux to the phenylpropanoid biosynthesis pathway, currently found solely in plants. In order to identify the resveratrol biosynthesis pathway in this strain at the gene level, de novo transcriptome sequencing was conducted using Illumina paired-end sequencing. A total of 22,954,434 high-quality reads were assembled into contigs and 18,570 unigenes were identified. Among these unigenes, 14,153 were annotated in the NCBI non-redundant protein database and 5341 were annotated in the Swiss-Prot database. After KEGG mapping, 2701 unigenes were mapped onto 115 pathways. Eighty-four unigenes were annotated in major pathways from glucose to resveratrol, coding 20 enzymes for glycolysis, 10 for phenylalanine biosynthesis, 4 for phenylpropanoid biosynthesis, and 4 for stilbenoid biosynthesis. Chalcone synthase was identified for resveratrol biosynthesis in this strain, due to the absence of stilbene synthase. All the identified enzymes indicated a reasonable biosynthesis pathway from glucose to resveratrol via glycolysis, phenylalanine biosynthesis, phenylpropanoid biosynthesis, and stilbenoid pathways. These results provide essential evidence for the occurrence of resveratrol biosynthesis in Alternaria sp. MG1 at the gene level, facilitating further elucidation of the molecular mechanisms involved in this strain's secondary metabolism.

Impact of cluster thinning on transcriptional regulation of anthocyanin biosynthesis-related genes in 'Summer Black' grapes

Cluster thinning is an agronomic practice that strongly affects anthocyanin biosynthesis in the skin of grape berries. However, the impact of cluster thinning on anthocyanin biosynthesis has not been fully elucidated at the molecular level. Here, we investigated its effects on the berry quality, the biosynthesis of anthocyanins, and the expression levels of related genes from the onset of véraison to harvest in 'Summer Black' grapes. It was observed that the total soluble solid and anthocyanin content in berry skin significantly increased under cluster thinning, whereas the berry weight and titratable acidity showed no differences from the beginning of véraison to harvest. The expression level of most anthocyanin biosynthesis-related genes was significantly up-regulated by cluster thinning from the beginning of véraison and was higher at its end compared to the control. Up-regulation of flavonoid 3',5'-hydroxylase (F3'5'H) and O-methyltransferase (OMT) expression, and down-regulation of flavonoid 3'-hydroxylase (F3'H) expression were observed, which might be the cause of shift in the anthocyanin profile. These findings provide insights into the molecular basis of the relationship between cluster thinning and anthocyanin biosynthesis in the grape berry skin.

Molecular cloning and identification of a flavanone 3-hydroxylase gene from Lycium chinense, and its overexpression enhances drought stress in tobacco

Flavonoids, as plant secondary metabolites, are widespread throughout the plant kingdom and involved in many physiological and biochemical processes. Drought resistance is attributed to flavonoids with respect to protective functions in the cell wall and membranes. The flavanone 3-hydroxylase (F3H) gene which encodes flavanone 3-hydroxylase, is essential in flavonoids biosynthetic pathway. Lycium chinense (L. chinense) is a deciduous woody perennial halophyte that grows under a large variety of environmental conditions and survives under extreme drought stress. A novel cDNA sequence coding a F3H gene in Lycium chinense (LcF3H, GenBank: KJ636468.1) was isolated. The open reading frame of LcF3H comprised 1101 bp encoding a polypeptide of 366 amino acids with a molecular weight of about 42 kDa and an isoelectric point of 5.32. The deduced LcF3H protein showed high identities with other plant F3Hs, and the conserved motifs were found in LcF3H at similar positions like other F3Hs. The recombinant protein converted naringen into dihydrokaempferol in vitro. Since studies have shown that amongst flavonoids, flavan-3-ols (catechin and epicatechin) have direct free radical scavenging activity to maintain the normal physiological function of cells in vivo, these data support the possible relationship between the oxidative damage and the regulation of LcF3H gene expression in L. chinense under drought stress. In order to better understand the biotechnological potential of LcF3H, gene overexpression was conducted in tobacco. The content of flavan-3-ols and the tolerance to drought stress were increased in LcF3H overexpressing tobacco. Analysis of transgenic tobacco lines also showed that antioxidant enzyme activities were increased meanwhile the malondialdehyde (MDA) content and the content of H2O2 were reduced comparing to nontransformed tobacco plants. Furthermore, the photosynthesis rate was less decreased in the transgenetic plants. These results suggest that LcF3H plays a role in enhancing drought tolerance in L. chinense, and its overexpression increases tolerance to drought stress by improving the antioxidant system in tobacco.

Light response and potential interacting proteins of a grape flavonoid 3'-hydroxylase gene promoter

Flavonoid 3'-hydroxylase (F3'H), a member of cytochrome P450 protein family, introduces B-ring hydroxyl group in the 3' position of the flavonoid. In this study, the cDNA sequence of a F3'H gene (VviF3'H), which contains an open reading frame of 1530 bp encoding a polypeptide of 509 amino acids, was cloned and characterized from Vitis vinifera L. cv. Cabernet Sauvignon. VviF3'H showed high homology to known F3'H genes, especially F3'Hs from the V. vinifera reference genome (Pinot Noir) and lotus. Expression profiling analysis using real-time PCR revealed that VviF3'H was ubiquitously expressed in all tested tissues including berries, leaves, flowers, roots, stems and tendrils, suggesting its important physiological role in plant growth and development. Moreover, the transcript level of VviF3'H gene in grape berries was relatively higher at early developmental stages and gradually decreased during véraison, and then increased in the mature phase. In addition, the promoter of VviF3'H was isolated by using TAIL-PCR. Yeast one-hybrid screening of the Cabernet Sauvignon cDNA library and subsequent in vivo/vitro validations revealed the interaction between VviF3'H promoter and several transcription factors, including members of HD-Zip, NAC, MYB and EIN families. A transcriptional regulation mechanism of VviF3'H expression is proposed for the first time.

Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars

Background

Grape cultivars and wines are distinguishable by their color, flavor and aroma profiles. Omic analyses (transcripts, proteins and metabolites) are powerful tools for assessing biochemical differences in biological systems.

Results

Berry skins of red- (Cabernet Sauvignon, Merlot, Pinot Noir) and white-skinned (Chardonnay, Semillon) wine grapes were harvested near optimum maturity (°Brix-to-titratable acidity ratio) from the same experimental vineyard. The cultivars were exposed to a mild, seasonal water-deficit treatment from fruit set until harvest in 2011. Identical sample aliquots were analyzed for transcripts by grapevine whole-genome oligonucleotide microarray and RNAseq technologies, proteins by nano-liquid chromatography-mass spectroscopy, and metabolites by gas chromatography-mass spectroscopy and liquid chromatography-mass spectroscopy. Principal components analysis of each of five Omic technologies showed similar results across cultivars in all Omic datasets. Comparison of the processed data of genes mapped in RNAseq and microarray data revealed a strong Pearson’s correlation (0.80). The exclusion of probesets associated with genes with potential for cross-hybridization on the microarray improved the correlation to 0.93. The overall concordance of protein with transcript data was low with a Pearson’s correlation of 0.27 and 0.24 for the RNAseq and microarray data, respectively. Integration of metabolite with protein and transcript data produced an expected model of phenylpropanoid biosynthesis, which distinguished red from white grapes, yet provided detail of individual cultivar differences. The mild water deficit treatment did not significantly alter the abundance of proteins or metabolites measured in the five cultivars, but did have a small effect on gene expression.

Conclusions

The five Omic technologies were consistent in distinguishing cultivar variation. There was high concordance between transcriptomic technologies, but generally protein abundance did not correlate well with transcript abundance. The integration of multiple high-throughput Omic datasets revealed complex biochemical variation amongst five cultivars of an ancient and economically important crop species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2115-y) contains supplementary material, which is available to authorized users.

Vitis vinifera L. Single-Nucleotide Polymorphism Detection with High-Resolution Melting Analysis Based on the UDP-Glucose:Flavonoid 3-O-Glucosyltransferase Gene

Vitis vinifera L. is a species with a large number of varieties, which differ in terms of anthocyanin content. The genes involved in the anthocyanin biosynthesis pathway have a direct effect in the anthocyanin profile of each variety, being potentially interesting for varietal identification. The current study aimed at the design of an assay suitable for the discrimination of the largest number of grapevine varieties. Two genes of the anthocyanin pathway, chalcone isomerase (CHI) and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT), were sequenced in 22 grapevine varieties. The CHI gene presented 5 SNPs within the sequence. A total of 58 SNPs and 1 INDEL were found among the UFGT gene, allowing the discrimination of 18 different genotypes within the 22 grapevine varieties. A HRM assay designed for UFGT, containing 704 bp, produced differentiated melting curves for each of the 18 haplotypes. The developed HRM assay is efficient in grapevine varietal discrimination.

Molecular and biochemical characterization of the UDP-glucose: Anthocyanin 5-O-glucosyltransferase from Vitis amurensis

Generally, red Vitis vinifera grapes only contain monoglucosidic anthocyanins, whereas most non-vinifera red grapes of the Vitis genus have both monoglucosidic and bis-glucosidic anthocyanins, the latter of which are believed to be more hydrophilic and more stable. Although previous studies have established the biosynthetic mechanism for formation of monoglucosidic anthocyanins, less attention has been paid to that of bis-glucosidic anthocyanins. In the present research, the full-length cDNA of UDP-glucose: anthocyanin 5-O-glucosyltransferase from Vitis amurensis Rupr. cv. 'Zuoshanyi' grape (Va5GT) was cloned. After acquisition and purification of recombinant Va5GT, its enzymatic parameters were systematically analyzed in vitro. Recombinant Va5GT used malvidin-3-O-glucoside as its optimum glycosidic acceptor when UDP-glucose was used as the glycosidic donor. Va5GT-GFP was found to be located in the cytoplasm by analyzing its subcellular localization with a laser-scanning confocal fluorescence microscope, and this result was coincident with its metabolic function of modifying anthocyanins in grape cells. Furthermore, the relationship between the transcriptional expression of Va5GT and the accumulation of anthocyanidin bis-glucosides during berry development suggested that Va5GT is a key enzyme in the biosynthesis of bis-glucosidic anthocyanins in V. amurensis grape berries.

Resveratrol: A Focus on Several Neurodegenerative Diseases

Molecules of the plant world are proving their effectiveness in countering, slowing down, and regressing many diseases. The resveratrol for its intrinsic properties related to its stilbene structure has been proven to be a universal panacea, especially for a wide range of neurodegenerative diseases. This paper evaluates (in vivo and in vitro) the various molecular targets of this peculiar polyphenol and its ability to effectively counter several neurodegenerative disorders such as Parkinson's, Alzheimer's, and Huntington's diseases and amyotrophic lateral sclerosis. What emerges is that, in the deep heterogeneity of the pathologies evaluated, resveratrol through a convergence on the protein targets is able to give therapeutic responses in neuronal cells deeply diversified not only in morphological structure but especially in their function performed in the anatomical district to which they belong.

Anthocyanin Accumulation and Molecular Analysis of Correlated Genes in Purple Kohlrabi (Brassica oleracea var. gongylodes L.)

Kohlrabi (Brassica oleracea var. gongylodes L.) is an important dietary vegetable cultivated and consumed widely for the round swollen stem. Purple kohlrabi shows abundant anthocyanin accumulation in the leaf and swollen stem. Here, different kinds of anthocyanins were separated and identified from the purple kohlrabi cultivar (Kolibri) by high-performance liquid chromatography-electrospray ionization tandem mass spectrometry. In order to study the molecular mechanism of anthocyanin biosynthesis in purple kohlrabi, the expression of anthocyanin biosynthetic genes and regulatory genes in purple kohlrabi and a green cultivar (Winner) was examined by quantitative PCR. In comparison with the colorless parts in the two cultivars, most of the anthocyanin biosynthetic genes and two transcription factors were drastically upregulated in the purple tissues. To study the effects of light shed on the anthocyanin accumulation of kohlrabi, total anthocyanin contents and transcripts of associated genes were analyzed in sprouts of both cultivars grown under light and dark conditions.

The State of the Art in Biosynthesis of Anthocyanins and Its Regulation in Pigmented Sweet Oranges [(Citrus sinensis) L. Osbeck]

Anthocyanins are water-soluble pigments belonging to the flavonoid compound family involved in nature in several aspects of plant development and defense. By bestowing much of the color and flavor on fruits and vegetables, they are components of the human diet and, thanks to their radical-scavenging properties, are not considered exclusively as food products but also as therapeutic agents. Several cultivars of red (or blood) oranges [Citrus sinensis (L.) Osbeck], such as Tarocco, Moro, and Sanguinello, are characterized by the presence of anthocyanins in both the rind and fruit juice vesicles. The amount and composition of anthocyanins in the pigmented orange cultivar vary greatly depending on variety, maturity, region of cultivation, and many other environmental conditions. Most of the blood orange varieties require a wide day-night thermal range to maximize color formation. Therefore, the production of red oranges characterized by high anthocyanin levels is limited to a few regions and in particular to the Sicilian area around Mount Etna in Italy, where the characteristic climate conditions yield fruits of unique color intensity and quality. In this review, both the basic information and the most recent advances in red orange anthocyanins are reported, with intense attention given to their biosynthesis and regulation.

Metabolic engineering for resveratrol derivative biosynthesis in Escherichia coli

We previously reported that the SbROMT3syn recombinant protein catalyzes the production of the methylated resveratrol derivatives pinostilbene and pterostilbene by methylating substrate resveratrol in recombinant E. coli. To further study the production of stilbene compounds in E. coli by the expression of enzymes involved in stilbene biosynthesis, we isolated three stilbene synthase (STS) genes from rhubarb, peanut, and grape as well as two resveratrol O-methyltransferase (ROMT) genes from grape and sorghum. The ability of RpSTS to produce resveratrol in recombinant E. coli was compared with other AhSTS and VrSTS genes. Out of three STS, only AhSTS was able to produce resveratrol from p-coumaric acid. Thus, to improve the solubility of RpSTS, VrROMT, and SbROMT3 in E. coli, we synthesized the RpSTS, VrROMT and SbROMT3 genes following codon-optimization and expressed one or both genes together with the cinnamate/4-coumarate:coenzyme A ligase (CCL) gene from Streptomyces coelicolor. Our HPLC and LC-MS analyses showed that recombinant E. coli expressing both ScCCL and RpSTSsyn led to the production of resveratrol when p-coumaric acid was used as the precursor. In addition, incorporation of SbROMT3syn in recombinant E. coli cells produced resveratrol and its mono-methylated derivative, pinostilbene, as the major products from p-coumaric acid. However, very small amounts of pterostilbene were only detectable in the recombinant E. coli cells expressing the ScCCL, RpSTSsyn and SbROMT3syn genes. These results suggest that RpSTSsyn exhibits an enhanced enzyme activity to produce resveratrol and SbROMT3syn catalyzes the methylation of resveratrol to produce pinostilbene in E. coli cells.

Salicylic acid induces alterations in the methylation pattern of the VaSTS1, VaSTS2, and VaSTS10 genes in Vitis amurensis Rupr. cell cultures

Salicylic acid (SA) treatment selectively reduced the cytosine DNA methylation of stilbene synthase ( STS ) genes and stimulated resveratrol production in cell cultures of Vitis amurensis. The effect of salicylic acid (SA) on plant growth, flowering time, and fruit number is known to correlate with the level of DNA methylation, while the potential correlation between SA-induced changes in DNA methylation and biosynthesis of secondary metabolites has not been studied. Trans-resveratrol, a naturally occurring plant phenol, has been reported to exhibit a wide range of valuable biological and pharmacological properties. In this study, cell cultures of Vitis amurensis capable of producing t-resveratrol were used as a model system to study whether the SA-induced increase in t-resveratrol production is associated with changes in DNA methylation of stilbene synthase (STS) genes. T-resveratrol is synthesized via the phenylpropanoid pathway, in which STS genes are the key enzymes. Treatment of V. amurensis callus cultures with SA significantly increased t-resveratrol production and the expression of certain STS genes (e.g., VaSTS2 and VaSTS10). A marked decrease in the methylation of the VaSTS2 and VaSTS10 genes in response to SA was demonstrated using bisulfite sequencing, while no considerable changes were detected in the methylation of VaSTS1, a constitutively and highly expressed STS gene. The obtained results show that SA treatment selectively reduced cytosine methylation of VaSTS genes. The data suggest that selective DNA demethylation of particular STS genes could be necessary for the activation of t-resveratrol biosynthesis in response to SA. This finding provides an insight into the mechanism of SA action and biosynthesis of secondary metabolites in plant cells.

Anthocyanin accumulation and transcriptional regulation of anthocyanin biosynthesis in purple bok choy (Brassica rapa var. chinensis)

Bok choy (Brassica rapa var. chinensis) is an important dietary vegetable cultivated and consumed worldwide for its edible leaves. The purple cultivars rich in health-promoting anthocyanins are usually more eye-catching and valuable. Fifteen kinds of anthocyanins were separated and identified from a purple bok choy cultivar (Zi He) by high-performance liquid chromatography-electrospray ionization tandem mass spectrometry. To investigate the molecular mechanisms underlying anthocyanin accumulation in bok choy, the expression profiles of anthocyanin biosynthetic and regulatory genes were analyzed in seedlings and leaves of the purple cultivar and the green cultivar (Su Zhouqing). Compared with the other tissues, BrTT8 and most of the anthocyanin biosynthetic genes were significantly up-regulated in the leaves and light-grown seedlings of Zi He. The results that heterologous expression of BrTT8 promotes the transcription of partial anthocyanin biosynthetic genes in regeneration shoots of tomato indicate that BrTT8 plays an important role in the regulation of anthocyanin biosynthesis.

The grapevine gene nomenclature system

BACKGROUND

Grapevine (Vitis vinifera L.) is one of the most important fruit crops in the world and serves as a valuable model for fruit development in woody species. A major breakthrough in grapevine genomics was achieved in 2007 with the sequencing of the Vitis vinifera cv. PN40024 genome. Subsequently, data on structural and functional characterization of grape genes accumulated exponentially. To better exploit the results obtained by the international community, we think that a coordinated nomenclature for gene naming in species with sequenced genomes is essential. It will pave the way for the accumulation of functional data that will enable effective scientific discussion and discovery. The exploitation of data that were generated independently of the genome release is hampered by their heterogeneous nature and by often incompatible and decentralized storage. Classically, large amounts of data describing gene functions are only available in printed articles and therefore remain hardly accessible for automatic text mining. On the other hand, high throughput "Omics" data are typically stored in public repositories, but should be arranged in compendia to better contribute to the annotation and functional characterization of the genes.

RESULTS

With the objective of providing a high quality and highly accessible annotation of grapevine genes, the International Grapevine Genome Project (IGGP) commissioned an international Super-Nomenclature Committee for Grape Gene Annotation (sNCGGa) to coordinate the effort of experts to annotate the grapevine genes. The goal of the committee is to provide a standard nomenclature for locus identifiers and to define conventions for a gene naming system in this paper.

CONCLUSIONS

Learning from similar initiatives in other plant species such as Arabidopsis, rice and tomato, a versatile nomenclature system has been developed in anticipation of future genomic developments and annotation issues. The sNCGGa's first outreach to the grape community has been focused on implementing recommended guidelines for the expert annotators by: (i) providing a common annotation platform that enables community-based gene curation, (ii) developing a gene nomenclature scheme reflecting the biological features of gene products that is consistent with that used in other organisms in order to facilitate comparative analyses.