Summary of Study ST003744
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 PR002330. The data can be accessed directly via it's Project DOI: 10.21228/M8FV76 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 | ST003744 |
| Study Title | A study exploring the epoxidation function of ODD enzymes (2-oxoglutarate/Fe(II)-dependent dioxygenases) |
| Study Summary | This study identified a series of ODD (2-oxoglutarate/Fe(II)-dependent dioxygenase) genes with potential C4β-C20 epoxidation activity from the Himalayan yew (Taxus wallichiana) genome. To validate their enzymatic functions, these genes were cloned into the Ycplac22 vector and expressed in a Saccharomyces cerevisiae strain engineered to produce taxadiene, the required substrate for ODD enzymes. The fermentation process involved initial culturing of the yeast strain in test tubes, followed by inoculation into fresh medium and the addition of n-dodecane and glucose to initiate two-phase fermentation, facilitating product separation and accumulation. After 4 days of cultivation, the upper organic phase was collected and analyzed by GC-MS, confirming the production of the target compound, 4β,20-taxadiene. The obtained GC-MS data were further used to assess whether the ODD enzymes exhibit potential epoxidation activity. |
| Institute | Northwestern Polytechnical University |
| Last Name | Li |
| First Name | Zhenzhu |
| Address | No. 127, Youyi West Road, Xi'an City |
| lizhenzhu@mail.nwpu.edu.cn | |
| Phone | 18829012174 |
| Submit Date | 2025-02-13 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | GC-MS |
| Release Date | 2025-02-24 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002330 |
| Project DOI: | doi: 10.21228/M8FV76 |
| Project Title: | A study exploring the epoxidation function of ODD enzymes (2-oxoglutarate/Fe(II)-dependent dioxygenases) |
| Project Type: | MS Qualitative Analysis |
| Project Summary: | This study identified a series of ODD (2-oxoglutarate/Fe(II)-dependent dioxygenase) genes with potential C4β-C20 epoxidation activity. To validate their enzymatic function, these genes were cloned into the Ycplac22 vector and introduced into Saccharomyces cerevisiae engineered to produce the necessary ODD substrate, taxadiene. The fermentation products were then analyzed using GC-MS to detect the formation of the target compound, 4β,20-taxadiene. |
| Institute: | Northwestern Polytechnical University |
| Last Name: | Li |
| First Name: | Zhenzhu |
| Address: | No. 127, Youyi West Road, Xi'an City |
| Email: | lizhenzhu@mail.nwpu.edu.cn |
| Phone: | 18829012174 |
Subject:
| Subject ID: | SU003876 |
| Subject Type: | Yeast |
| Subject Species: | Taxus wallichiana |
| Taxonomy ID: | 147273 |
Factors:
Subject type: Yeast; Subject species: Taxus wallichiana (Factor headings shown in green)
| mb_sample_id | local_sample_id | Gene |
|---|---|---|
| SA408181 | CK | Control |
| SA408182 | GENE1 | GENE1 |
| SA408183 | GENE10 | GENE10 |
| SA408184 | GENE13 | GENE13 |
| SA408185 | GENE14 | GENE14 |
| SA408186 | GENE15 | GENE15 |
| SA408187 | GENE16 | GENE16 |
| SA408188 | GENE2 | GENE2 |
| SA408189 | GENE3 | GENE3 |
| SA408190 | GENE6 | GENE6 |
| SA408191 | GENE7 | GENE7 |
| SA408192 | GENE9 | GENE9 |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO003869 |
| Collection Summary: | GENE1-GENE16, a series of novel genes with potential epoxidation activity, were newly identified from the genome of the Himalayan yew (Taxus wallichiana), whose sequences are provided in the downloadable file "nucleotide_sequences_of_11_ODD_candidate_genes.csv". These putative ODD genes were subsequently assembled into the yeast expression vector Ycplac22. The constructed expression vector was then transformed into a pre-engineered Saccharomyces cerevisiae chassis strain, which was designed for cytoplasmic production of taxa-4(5),11(12)-diene (taxadiene), where the genes were expressed and their functions analyzed. The yeast strains were inoculated into 40 mL of fresh medium at a 1:50 ratio. A two-phase fermentation process was initiated and maintained at 30°C with agitation at 220 rpm for 4 days. After fermentation, the culture was centrifuged at 3600 rpm for 10 minutes, and the upper organic phase was collected for further analysis. |
| Sample Type: | Yeast cells |
Treatment:
| Treatment ID: | TR003885 |
| Treatment Summary: | After 10 hours of yeast cultivation, 5 mL of n-dodecane and 2 mL of 40% glucose were added to the culture. |
Sample Preparation:
| Sampleprep ID: | SP003882 |
| Sampleprep Summary: | The collected upper organic phase was filtered and subsequently subjected to GC-MS analysis. |
Chromatography:
| Chromatography ID: | CH004669 |
| Methods Filename: | TS_Method.pdf |
| Instrument Name: | Thermo Scientific TSQ 9000 |
| Column Name: | ThermoFisher TraceGOLD TG-1MS (30m x 0.25mm, 0.25um) |
| Column Temperature: | 300 |
| Flow Gradient: | - |
| Flow Rate: | 20mL/min |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | GC |
Analysis:
| Analysis ID: | AN006148 |
| Analysis Type: | MS |
| Acquisition Parameters File: | TS_Method.pdf |
| Chromatography ID: | CH004669 |
| Num Factors: | 12 |
| Num Metabolites: | 1 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST003744_AN006148_Results.txt |
| Units: | Intensity |
