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 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN005207 | AN005208 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Waters Acquity | Waters Acquity |
| Column | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole |
| MS instrument name | Waters Xevo TQ-XS | Waters Xevo TQ-XS |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | mg/L | mg/L |
Chromatography:
| Chromatography ID: | CH003940 |
| Chromatography Summary: | Ultraperformance liquid chromatography was performed on a Waters Acquity UPLC system (Milford, MA) consisting of a binary pump, an online vacuum degasser, an autosampler, and a column compartment. Separation of the phenolic compounds was achieved on a Waters Acquity HSS T3 column 1.8 μm, 100 mm × 2.1 mm (Milford, MA, USA), kept at 40 °C. Mobile phase A was water containing 0.1% formic acid; mobile phase B was acetonitrile containing 0.1% formic acid. The flow was 0.4 mL/min, and the gradient profile was 0-0.1 min, 5% B; from 0 to 3 min, linear gradient to 20% B; from 3 to 4.3 min, isocratic 20% B; from 4.3 to 9 min, linear gradient to 45% B; from 9 to 11 min, linear gradient to 100% B; from 11 to 13 min, wash at 100% B; from 13.01 to 15 min, back to the initial conditions of 5% B. The injection volume of both the standard solutions and the samples was 2 μL. After each injection, the needle was rinsed with 600 μL of weak wash solution (water/methanol, 90:10) and 200 μL of strong wash solution (methanol/water, 90:10). Samples were kept at 6 °C during the analysis. |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0-0.1 min: 5% B, 0.1-3.0 min: linear 20%B, 3.0-4.3 min: isocratic 20% B, 4.3-9.0 min: linear 45% B, 9.0-11.0 min: linear 100% B, 11.0-13.0 min: wash 100% B, 13.01 – 15.0 min: back to initial 5% B |
| Flow Rate: | 0.4 ml/min |
| Solvent A: | 99.9% water/0.1% formic acid |
| Solvent B: | 99.9% acetonitrile/0.1% formic acid |
| Chromatography Type: | Reversed phase |
