Direct regulation of shikimate, early phenylpropanoid and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine
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PROVIDER: PRJNA801617 | ENA |
REPOSITORIES: ENA
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Project description:Direct regulation of shikimate, early phenylpropanoid and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine
| PRJNA748348 | ENA
Project description:The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway, but the extent of this control has not been deeply studied. Here we demonstrate how DNA affinity purification sequencing (DAP-Seq) allows for genome-wide TF binding site interrogation in grape. We obtained 5,190 and 4,443 binding events assigned to 4,041 and 3,626 genes for MYB14 and MYB15, respectively (around 40% of peaks located within -10kb of transcription start sites). DAP-Seq of MYB14/MYB15 was combined with aggregate gene co-expression networks (GCNs) built from more than 1,400 transcriptomic datasets from leaves, fruits and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15 and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 out of 47 STS family genes. Moreover, all three MYBs bind to several PAL, C4H and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co-regulator and resveratrol-modifying gene candidates amongst which ROMT2-3 were validated enzymatically. A high proportion of DAP-Seq bound genes was induced in the activated transcriptomes of transient MYB15-overexpressing grapevine leaves, validating our methodological approach for delimiting TF targets. Overall, Subgroup 2 R2R3-MYBs appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production. The integration of DAP-Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome-wide approaches in the context of non-model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism.
2022-01-10 | GSE180450 | GEO
Project description:A set of grapevine R2R3 MYB repressors negatively regulate the expression of genes involved in different branches of the phenylpropanoid pathway
2014-09-30 | GSE58742 | GEO
Project description:A set of grapevine R2R3 MYB repressors negatively regulate the expression of genes involved in different branches of the phenylpropanoid pathway For the genetic transformation of Vitis vinifera cv Maccabeu, the in vitro plantlets were grown for 90 days under light and temperature controlled. For overexpression of VvMYBC2-L3 in Vitis vinifera cv Maccabeu hairy roots, the cDNA sequence was transferred into the binary vector pH2GW7 by site-specific recombination. The construct was then inserted into Agrobacterium tumefaciens A4 by electroporation and used for the grapevine transformation. The induction and culture of transgenic HRs in grapevine were performed as described by Torregrosa and Bouquet (1997), with modifications reported in Cutanda-Perez et al. (2009).
2014-09-30 | E-GEOD-58742 | biostudies-arrayexpress
Project description:We cloned and characterized a subgroup S4 R2R3 Myb transcription factor, PgMyb308-like. Overexpressing PgMyb308-like in pomegranate hairy roots. Transcriptome analysis of PgMyb308-like-overexpressing hairy roots revealed reprogramming of cell wall-related genes, while overexpression of PgMyb308-like in Arabidopsis thaliana plants uncovered its distinct role in a different genetic and metabolic background. The results suggest that PgMyb308-like activates genes in the shikimate pathway and lignin biosynthesis, but suppresses those involved in the production of HTs and flavonoids.
2022-05-25 | GSE178072 | GEO
Project description:V. vinifera cv. ‘Shiraz’ leaves from 10-week old plants were transformed via Agrobacterium-mediated infiltration with MYB15 (35S::VviMYB15) or an empty vector control. Samples were subsequently collected at five different time points (8h, 24h, 48h, 72h and 96h) in separate replicate pools (L1 and L2) consisting of three leaves from independent plants per time-point (n=2 biological replicates). Microarray analysis, using the Affymetrix V. vinifera Grape Array (A-AFFY-78), was carried out on extracted leaf RNA from three of the time points described for both control and MYB15 infiltrated samples.
2022-01-29 | GSE195646 | GEO
Project description:Grapevine is a commercially important fruit crop that provides berries for direct consumption, juice pressing, drying (raisins), and fermentation to produce wine. The economic value of the crop has encouraged many researchers to study the physiological and molecular basis of berry development, particularly processes that affect wine quality. Post-harvest withering of grapevine berries is used in the production of dessert and fortified wines to alter must quality characteristics and to increase the concentration of simple sugars.
2010-09-24 | GSE20511 | GEO
Project description:The molecular events that characterize postripening grapevine berries have rarely been investigated and are poorly defined. In particular, a detailed definition of changes occurring during the postharvest dehydration, a process undertaken to make some particularly special wine styles, would be of great interest for both winemakers and plant biologists. We report an exhaustive survey of transcriptomic and metabolomic responses in berries representing six grapevine genotypes subjected to postharvest dehydration under identical controlled conditions. The modulation of phenylpropanoid metabolism clearly distinguished the behavior of genotypes, with stilbene accumulation as the major metabolic event, although the transient accumulation/depletion of anthocyanins and flavonols was the prevalent variation in genotypes that do not accumulate stilbenes. The modulation of genes related to phenylpropanoid/stilbene metabolism highlighted the distinct metabolomic plasticity of genotypes, allowing for the identification of candidate structural and regulatory genes. In addition to genotype-specific responses, a core set of genes was consistently modulated in all genotypes, representing the common features of berries undergoing dehydration and/or commencing senescence. This included genes controlling ethylene and auxin metabolism as well as genes involved in oxidative and osmotic stress, defense responses, anaerobic respiration, and cell wall and carbohydrate metabolism. Several transcription factors were identified that may control these shared processes in the postharvest berry. Changes representing both common and genotype-specific responses to postharvest conditions shed light on the cellular processes taking place in harvested berries stored under dehydrating conditions for several months.
2017-01-09 | GSE75498 | GEO
Project description:Sonic Hedgehog subgroup medulloblastomas
| PRJNA384622 | ENA
Project description:Grapevine red blotch is a recently identified viral disease that was first recognized in the Napa Valley of California. Infected plants showed foliar symptoms similar to leafroll, another grapevine viral disease, on vines testing negative for known grapevine leafroll-associated virus. Later, the Grapevine red blotch virus (GRBV) was independently discovered in the US states of California and New York and was demonstrated to be the causal agent of red blotch disease. Due to its wide occurrence in the US, vector transmission and impacts on grape industry, this virus has the potential to cause serious economic losses. Despite numerous attempts, it was not possible to isolate or visualize viral particles from GRBV infected plants. Consequently, this has hampered the development of a serological assay that would facilitate GRBV detection in grapevine. We therefore decided to explore mass spectrometry approaches in order to quantify GRBV in infected plants and to identify potential biomarkers for viral infection. We present for the first time the physical detection on the protein level of the two GRBV genes V1 (coat protein) and V2 in grapevine tissue lysates. The GRBV coat protein load in leaf petioles was determined to be in the range of 100 to 900 million copies per milligram wet weight by using three heavy isotope labeled reference peptides as internal standards. The V1 copy number per unit wet tissue weight in leaves appeared to be about six times lower, and about 200-times lower in terms of protein concentration in the extractable protein mass than in petioles. We found a consistent upregulation of several enzymes involved in flavonoid biosynthesis in leaf and petiole extracts of GRBV-infected plants by label-free shotgun proteomics, indicating the activation of a defense mechanism against GRBV, a plant response already described for grapevine leafroll associated virus infection on the transcriptome level. Last but not least, we identified some other microorganisms belonging to the grapevine leaf microbiota, two bacterial species (Novosphingobium sp. Rr 2-17 and Methylobacterium) and one virus, Grapevine rupestris stem pitting associated virus.
2018-12-19 | PXD011002 | Pride