Summary of Study ST003173
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001973. The data can be accessed directly via it's Project DOI: 10.21228/M8PQ8C This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003173 |
| Study Title | Assessment and partial characterization of candidate genes in dihydrochalcone and arbutin biosynthesis in an apple-pear hybrid by de novo transcriptome assembly |
| Study Summary | The goal of the study was to determine the phenolic profile of young and old leaves, as well as fruit of apple (Malus x domestica), pear (Pyrus communis) and an intergeneric apple-pear hybrid. Three independent replicates were obtained for each genotype from the germplasm collection at Fondazione Edmund Mach (Italy) and analyzed by a targeted phenolic LC/MS-MS method. In addition, candidate genes from apple, pear and apple-pear hybrid retrieved from a de novo transcriptome assembly were expressed in E. coli and recombinant proteins were tested (in triplicate) to determine the conversion of hydroquinone to arbutin. Combining RNA-Seq, in silico functional annotation prediction, targeted gene expression analysis and expression – metabolite correlations with the data submitted to Metabolomics Workbench, we identified candidate genes for functional characterisation, resulting in the identification of active arbutin synthases in the hybrid and parental genotypes. We found that the putative arbutin synthases of pear (PcAS) and apple-pear hybrid (HybAS) were able to convert hydroquinone into arbutin. Interestingly, also one out of two putative arbutin synthases isolated from apple (MdAS1) could produce arbutin in vitro. However, the metabolomic profiling of phenolic compounds showed that apple lacks of arbutin and was found to accumulate the precursor hydroquinone in traces in young and old leaves of apple. Although quercetin was accumulated in similar amounts in the same tissues, a luminiscence-based assay showed that quercetin was converted only 25% compared to activity towards hydroquinone in the tested conditions. In summary, the metabolomic profiling submitted to Metabolomics workbench also shows that: 1) arbutin is accumulated mainly in young leaves of pear, followed by the apple-pear hybrid and was found in traces in apple fruit; 2) rutin was found mainly in pear and apple-pear hybrid tissues; 3) phenolic profile of apple is dominated by phloridzin and undetectable in all pear tissues analyzed, with young leaves being the tissue showing highest accumulation. |
| Institute | Fondazione Edmund Mach |
| Last Name | Miranda Chavez |
| First Name | Simon David |
| Address | Via Mach, 1, San Michele all'Adige, Trento, 38098, Italy |
| simondavid.mirandachavez@fmach.it | |
| Phone | +390461615231 |
| Submit Date | 2024-04-12 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-05-03 |
| Release Version | 1 |
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Collection:
| Collection ID: | CO003285 |
| Collection Summary: | For metabolite profiling, ripe fruit and young and old leaves of apple, pear and hybrid were collected from each individual maintained in the germplasm collection of Fondazione Edmund Mach. 100 mg of fresh tissue (FW) was extracted in 4 mL 80% v·v-1 methanol, sonicated for 20 min at 60 Hz in a water bath at 25ºC, agitated for further 20 min and kept in dark for 48 h, filtered through a 0.22 µm PTFE filter and stored at 4 ºC. For enzyme assays, E. coli strains harbouring pGEX-4T-1 with putative AS were grown in Terrific Broth (12 g·L-1 tryptone, 24 g·L-1 yeast extract, 9.4 g·L-1 K2HPO4, 2.2 g·L-1 KH2PO4, 4 mL·L-1 glycerol) at 37 °C and recombinant proteins were induced by supplementation of 0.5 mM IPTG at optical density OD600 of 0.5 – 0.6 and incubation at 20 ºC with agitation at 200 rpm for 16 h. Protein extraction was carried out by resuspending cells with B-PER™ Complete reagent supplemented with cOmplete™ protease inhibitor cocktail (Roche) followed by protein purification by Pierce™ GST spin purification kit, according to manufacter’s instructions. Quantitation of proteins was carried out by Pierce™ BCA protein assay kit and Bradford reagent (Sigma) after crude extraction and Glutathione S-Transferase (GST) - fusion protein purification, respectively. Enzyme activity was assayed in 200 µL reactions using 1 mM hydroquinone, 2 mM UDP-glucose, 5 µg purified protein in 200 mM Tris HCl, pH 7.5 buffer, incubated at 50 °C for 1 h and terminated by adding 300 µL methanol, as previously described35. |
| Sample Type: | Plant tissue/Enzyme assay |
| Storage Conditions: | -80℃ |
