Summary of Study ST003342
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 PR002078. The data can be accessed directly via it's Project DOI: 10.21228/M8124D 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 | ST003342 |
| Study Title | Glucosinolate profile and specifier protein activity determine the glucosinolate hydrolysis product formation in kohlrabi (Brassica oleracea var. gongylodes) in a tissue-specific way |
| Study Summary | Glucosinolates, commonly found in Brassica vegetables, are hydrolyzed by myrosinase to form bioactive isothiocyanates unless specifier proteins redirect the degradation to less bioactive nitriles and epithionitriles. Here, the tissue-specific impact of specifier proteins on the outcome of glucosinolate hydrolysis in nine kohlrabi tissues was investigated. Glucosinolate and their hydrolysis product profiles, epithiospecifier protein and myrosinase activity and protein abundance patterns of key glucosinolate biosynthesis, transport and hydrolysis proteins were determined and correlated to the metabolites in the kohlrabi tissues. Leaf tissues were rich in glucoraphanin, while bulb tissues contained more glucoerucin. Moreover, a higher proportion of isothiocyanates was formed in leaf stalk, bulb peel, stem and root, tissues with relatively higher ESM1 abundance and a higher ratio of myrosinase activity to ESP activity. This study shows that tissue-specific glucosinolate hydrolysis is mediated by glucosinolate biosynthesis and profiles, myrosinase activity and specifier protein as well as modifier protein abundance. |
| Institute | Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V. |
| Last Name | Hanschen |
| First Name | Franziska |
| Address | Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Brandenburg, Germany |
| hanschen@igzev.de | |
| Phone | 00493370178250 |
| Submit Date | 2024-07-12 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | GC-MS |
| Release Date | 2024-11-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002078 |
| Project DOI: | doi: 10.21228/M8124D |
| Project Title: | Glucosinolate profile and specifier protein activity determine the glucosinolate hydrolysis product formation in kohlrabi (Brassica oleracea var. gongylodes) in a tissue-specific way |
| Project Summary: | Glucosinolates, commonly found in Brassica vegetables, are hydrolyzed by myrosinase to form bioactive isothiocyanates unless specifier proteins redirect the degradation to less bioactive nitriles and epithionitriles. Here, the tissue-specific impact of specifier proteins on the outcome of glucosinolate hydrolysis in nine kohlrabi tissues was investigated. Glucosinolates and their hydrolysis product profiles, epithiospecifier protein and myrosinase activity and protein abundance patterns of key glucosinolate biosynthesis, transport and hydrolysis proteins were determined and correlated to the metabolites in the kohlrabi tissues. Leaf tissues were rich in glucoraphanin, while bulb tissues contained more glucoerucin. Moreover, a higher proportion of isothiocyanates was formed in leaf stalk, bulb peel, stem and root, tissues with relatively higher ESM1 abundance and a higher ratio of myrosinase activity to ESP activity. This study shows that tissue-specific glucosinolate hydrolysis is mediated by glucosinolate biosynthesis and profiles, myrosinase activity and specifier protein as well as modifier protein abundance. |
| Institute: | Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V. |
| Department: | Plant Quality and Food Security |
| Last Name: | Hanschen |
| First Name: | Franziska |
| Address: | Theodor-Echtermeyer-Weg 1 |
| Email: | hanschen@igzev.de |
| Phone: | 00493370178250 |
| Funding Source: | Leibniz Association |
| Project Comments: | J16/2017 |
Subject:
| Subject ID: | SU003463 |
| Subject Type: | Plant |
| Subject Species: | Brassica oleracea |
| Genotype Strain: | Brassica oleracea var. gongylodes cv. 'Kolibri' |
| Age Or Age Range: | adult |
| Species Group: | Plants |
Factors:
Subject type: Plant; Subject species: Brassica oleracea (Factor headings shown in green)
| mb_sample_id | local_sample_id | Tissue |
|---|---|---|
| SA364633 | K25 | Bulb core |
| SA364634 | K22 | Bulb core |
| SA364635 | K23 | Bulb core |
| SA364636 | K24 | Bulb core |
| SA364637 | K21 | Bulb core |
| SA364638 | K304 | Bulb core |
| SA364639 | K303b | Bulb core |
| SA364640 | K302 | Bulb core |
| SA364641 | K301 | Bulb core |
| SA364642 | K300 | Bulb core |
| SA364643 | K305 | Bulb middle part |
| SA364644 | K306 | Bulb middle part |
| SA364645 | K307 | Bulb middle part |
| SA364646 | K29 | Bulb middle part |
| SA364647 | K28 | Bulb middle part |
| SA364648 | K27 | Bulb middle part |
| SA364649 | K30 | Bulb middle part |
| SA364650 | K26 | Bulb middle part |
| SA364651 | K308 | Bulb middle part |
| SA364652 | K309 | Bulb middle part |
| SA364653 | K310 | Bulb peel |
| SA364654 | K311 | Bulb peel |
| SA364655 | K314 | Bulb peel |
| SA364656 | K312 | Bulb peel |
| SA364657 | K31 | Bulb peel |
| SA364658 | K32 | Bulb peel |
| SA364659 | K33 | Bulb peel |
| SA364660 | K34 | Bulb peel |
| SA364661 | K35 | Bulb peel |
| SA364662 | K313 | Bulb peel |
| SA364663 | K287 | Leaf lamina |
| SA364664 | K288 | Leaf lamina |
| SA364665 | K289 | Leaf lamina |
| SA364666 | K7 | Leaf lamina |
| SA364667 | K6 | Leaf lamina |
| SA364668 | K9 | Leaf lamina |
| SA364669 | K8 | Leaf lamina |
| SA364670 | K10 | Leaf lamina |
| SA364671 | K286 | Leaf lamina |
| SA364672 | K285 | Leaf lamina |
| SA364673 | K11 | Leaf margin |
| SA364674 | K12 | Leaf margin |
| SA364675 | K13 | Leaf margin |
| SA364676 | K294 | Leaf margin |
| SA364677 | K293 | Leaf margin |
| SA364678 | K292 | Leaf margin |
| SA364679 | K291 | Leaf margin |
| SA364680 | K290 | Leaf margin |
| SA364681 | K14 | Leaf margin |
| SA364682 | K15 | Leaf margin |
| SA364683 | K1 | Leaf midvein |
| SA364684 | K284 | Leaf midvein |
| SA364685 | K283 | Leaf midvein |
| SA364686 | K3 | Leaf midvein |
| SA364687 | K4 | Leaf midvein |
| SA364688 | K5 | Leaf midvein |
| SA364689 | K280 | Leaf midvein |
| SA364690 | K2 | Leaf midvein |
| SA364691 | K281 | Leaf midvein |
| SA364692 | K282 | Leaf midvein |
| SA364693 | K18 | Leaf stalk |
| SA364694 | K16 | Leaf stalk |
| SA364695 | K19 | Leaf stalk |
| SA364696 | K20 | Leaf stalk |
| SA364697 | K17 | Leaf stalk |
| SA364698 | K299 | Leaf stalk |
| SA364699 | K298b | Leaf stalk |
| SA364700 | K297 | Leaf stalk |
| SA364701 | K296 | Leaf stalk |
| SA364702 | K295 | Leaf stalk |
| SA364703 | K323 | Root |
| SA364704 | K324 | Root |
| SA364705 | K321 | Root |
| SA364706 | K320 | Root |
| SA364707 | K322 | Root |
| SA364708 | K44 | Root |
| SA364709 | K43 | Root |
| SA364710 | K45 | Root |
| SA364711 | K41 | Root |
| SA364712 | K42 | Root |
| SA364713 | K37 | Stem |
| SA364714 | K315 | Stem |
| SA364715 | K316 | Stem |
| SA364716 | K317 | Stem |
| SA364717 | K318 | Stem |
| SA364718 | K319 | Stem |
| SA364719 | K38 | Stem |
| SA364720 | K39 | Stem |
| SA364721 | K40 | Stem |
| SA364722 | K36 | Stem |
| Showing results 1 to 90 of 90 |
Collection:
| Collection ID: | CO003456 |
| Collection Summary: | The kohlrabi plants were harvested at maturity (68 days after sowing). Nine organs were harvested from each kohlrabi plant (Figure 1B). Regarding the leaf tissues, the third youngest leaf was harvested and separated into four parts (leaf midvein, leaf lamina, leaf margin and leaf stalk). Further, three parts of the bulb (bulb core, bulb middle part and bulb peel) the stem and the root were harvested as well (Figure 1B). Five biological replicates for each plant organ were prepared comprising of three pooled plants. The harvested plant organ materials were weighed, put into 20 mL vials (polyvial V; Zinsser Analytics GmbH, Eschborn, Germany), immediately flash frozen in liquid nitrogen, stored at −20 °C and then subsequently freeze-dried. For the homogenization metal balls (8 mm ⌀) were added to each vial and the samples were ground to a fine powder within 2 min using a mixer mill at 30 Hz (MM400, Retsch GmbH, Haan, Germany). The kohlrabi stem sample which was tough, was allowed to cool (at room temperature) and the grinding was repeated to get the fine powder. The samples were then stored at −20 °C until the subsequent experiments. The whole experiment was performed two times independently. |
| Collection Protocol Filename: | ProtocolKohlrabi.pdf |
| Sample Type: | Plant |
Treatment:
| Treatment ID: | TR003472 |
| Treatment Summary: | The seeds of kohlrabi (B. oleracea var. gongylodes cv. Kolibri) obtained from Bejo Samen GmbH, (Sonsbeck, Germany) were grown in seed trays and then transferred to single 15 cm diameter polypropylene pots containing soil (Einheitserde T, Einheitserde Werkverband e.V., Germany) after germination. The plants were grown under controlled growth conditions in a phytochamber (ENGIE Deutschland GmbH, Köln, Germany) with mercury to metal halide conversion lamp (Clean Ace (Daylight) Mogul Base, 6500K CCT/90CRI; EYE Lighting International, Mentor, OH) at the Leibniz Institute of Vegetable and Ornamental Crops in Großbeeren, Germany. The following growth conditions were used: temperature 22 °C to 18 °C (day to night), 12 h photoperiod, light intensity 500 μmol m−2 s−1 and 70 % air humidity. The plants were watered as needed and no fertilizer was added during the growth period. |
Sample Preparation:
| Sampleprep ID: | SP003470 |
| Sampleprep Summary: | The volatile glucosinolate (GLS) hydrolysis products were extracted from the homogenized plant material and quantified according to Friedrich, Wermter, Andernach, Witzel, and Hanschen (2022) with small modifications. Briefly, 250 µL of water was added to 25 mg of freeze-dried material and incubated for one hour at room temperature. After incubation, the GLS hydrolysis products were then extracted with methylene chloride three times (with 2 mL in the first and 1.5 mL in the second and third extraction step) in the presence of 0.2 µmol benzonitrile internal standard. After each extraction steps, samples were centrifuged and the methylene chloride phase was then filtered over anhydrous sodium sulfate, collected and finally concentrated under a nitrogen stream to 300 µL. Reference: Friedrich, K., Wermter, N. S., Andernach, L., Witzel, K., & Hanschen, F. S. (2022). Formation of volatile sulfur compounds and S-methyl-L-cysteine sulfoxide in Brassica oleracea vegetables. Food Chemistry, 383, 132544. |
| Sampleprep Protocol Filename: | ProtocolKohlrabi.pdf |
Chromatography:
| Chromatography ID: | CH004160 |
| Chromatography Summary: | The volatile compounds were analyzed by gas chromatography mass spectrometry (GC-MS) system (7890 A GC with 5975C Inert XL MSD, Agilent Technologies Deutschland GmbH, Waldbronn, Germany) by using a SGE BPX5 column (30 m × 0.25 mm × 0.25 μm) (Trajan Scientific Europe Ltd., Victoria, Australia). After splitless injection of 1 µL of sample solution at 190°C, analytes were separated with He as carrier gas (1.8 mL/min) and a temperature gradient starting at 37°C (for 3 min) rising with 9°C/min to 90°C (2 min hold) then to 110°C with 3°C/min, further increased to 210°C with 9°C/min, then to 223°C with 3°C/min, then to 230°C with 9°C/min and finally the GC was heated to 310°C with 35°C/min (6 min hold). |
| Instrument Name: | Agilent 7890A |
| Column Name: | SGE BPX5 (30m × 0.25mm; 0.25um) |
| Column Temperature: | starting at 37°C (for 3 min) rising with 9°C/min to 90°C (2 min hold) then to 110°C with 3°C/min, further increased to 210°C with 9°C/min, then to 223°C with 3°C/min, then to 230°C with 9°C/min and finally the GC was heated to 310°C with 35°C/min (6 min hold) |
| Flow Gradient: | - |
| Flow Rate: | - |
| Solvent A: | - |
| Solvent B: | - |
| Chromatography Type: | GC |
Analysis:
| Analysis ID: | AN005477 |
| Analysis Type: | MS |
| Analysis Protocol File: | ProtocolKohlrabi.pdf |
| Chromatography ID: | CH004160 |
| Num Factors: | 9 |
| Num Metabolites: | 12 |
| Units: | µmol/g dry weight of tissue |
