Summary of Study ST002541
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 PR001637. The data can be accessed directly via it's Project DOI: 10.21228/M83M7P 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 | ST002541 |
| Study Title | Methionine restriction constrains lipoylation and activates mitochondria for nitrogenic synthesis of amino acids (Part 1) |
| Study Summary | Methionine restriction (MR) provides metabolic benefits in many organisms. However, mechanisms underlying the MR-induced effect remain incompletely understood. Here, we show in the budding yeast S. cerevisiae that MR relays a signal of S-adenosylmethionine (SAM) deprivation to adapt bioenergetic mitochondria to nitrogenic anabolism. In particular, decreases in cellular SAM constrain lipoate metabolism and protein lipoylation required for the operation of the tricarboxylic acid (TCA) cycle in the mitochondria, leading to incomplete glucose oxidation with an exit of acetyl-CoA and alpha-ketoglutarate from the TCA cycle to the syntheses of amino acids, such as arginine and leucine. This mitochondrial SAM-induced response, namely mitoSIR, promotes cell fitness through the coordination of mitochondrial fuel metabolism with the nitrogenic synthesis of amino acids. |
| Institute | ZheJiang University |
| Department | Life Sciences Institute |
| Last Name | Cunqi |
| First Name | Ye |
| Address | 866 Yuhangtang Rd, Hangzhou 310058, P.R. China |
| yecunqi@zju.edu.cn | |
| Phone | 15267181160 |
| Submit Date | 2023-04-05 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-04-21 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001637 |
| Project DOI: | doi: 10.21228/M83M7P |
| Project Title: | The metabolomics analysis of Methionine restriction |
| Project Type: | targeted metabolomics data |
| Project Summary: | Methionine restriction (MR) provides metabolic benefits in many organisms. However, mechanisms underlying the MR-induced effect remain incompletely understood. Here, we show in the budding yeast S. cerevisiae that MR relays a signal of S-adenosylmethionine (SAM) deprivation to adapt bioenergetic mitochondria to nitrogenic anabolism.In particular, decreases in cellular SAM constrain lipoate metabolism and protein lipoylation required for the operation of the tricarboxylic acid (TCA) cycle in the mitochondria, leading to incomplete glucose oxidation with an exit of acetyl-CoA and alpha-ketoglutarate from the TCA cycle to the syntheses of amino acids, such as arginine and leucine. This mitochondrial SAM-induced response, namely mitoSIR, promotes cell fitness through the coordination of mitochondrial fuel metabolism with the nitrogenic synthesis of amino acids. |
| Institute: | Zhejiang University |
| Department: | Life Sciences Institute |
| Last Name: | Cunqi |
| First Name: | Ye |
| Address: | 866 Yuhangtang Rd, Hangzhou 310058, P.R. China |
| Email: | yecunqi@zju.edu.cn |
| Phone: | 15267181160 |
Subject:
| Subject ID: | SU002641 |
| Subject Type: | Yeast |
| Subject Species: | Saccharomyces cerevisiae |
| Taxonomy ID: | 4932 |
| Genotype Strain: | CEN.P.K |
Factors:
Subject type: Yeast; Subject species: Saccharomyces cerevisiae (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample Type |
|---|---|---|
| SA255560 | met6KO_0h_1 | 0h |
| SA255561 | met6KO_0h_3 | 0h |
| SA255562 | met6KO_0h_2 | 0h |
| SA255563 | met6KO_15h_3 | 15h |
| SA255564 | met6KO_15h_2 | 15h |
| SA255565 | met6KO_15h_1 | 15h |
| SA255566 | met6KO_2h_2 | 2h |
| SA255567 | met6KO_2h_1 | 2h |
| SA255568 | met6KO_2h_3 | 2h |
| SA255569 | met6KO_4h_2 | 4h |
| SA255570 | met6KO_4h_1 | 4h |
| SA255571 | met6KO_4h_3 | 4h |
| SA255572 | met6KO_6h_1 | 6h |
| SA255573 | met6KO_6h_2 | 6h |
| SA255574 | met6KO_6h_3 | 6h |
| Showing results 1 to 15 of 15 |
Collection:
| Collection ID: | CO002634 |
| Collection Summary: | Care was taken to quench cells quickly in -40℃ and maintain metabolites in acid to minimize oxidation |
| Sample Type: | Yeast cells |
Treatment:
| Treatment ID: | TR002653 |
| Treatment Summary: | Mutant MET6KO cells were cultured in SD medium with the supplements of Met and growed to log phase, then cells were washed with normal SD medium and re-cultured in SD medium |
Sample Preparation:
| Sampleprep ID: | SP002647 |
| Sampleprep Summary: | Briefly, equal OD units of cells were rapidly quenched to stop metabolism by addition into 4 volumes of quenching buffer containing 60% methanol and 10 mM Tricine, pH 7.4 that was pre-cooled to -40°C. 5 min after holding at -40°C, cells were spun at 5,000 g for 3 min at 0°C, washed with the same buffer, and then resuspended in 1 mL extraction buffer containing 75% ethanol and 0.5 mM Tricine, pH 7.4. Intracellular metabolites were extracted by incubating at 75°C for 3 min, followed by chilling on ice for 5 min. Samples were spun at 20,000 g for 1 min to pellet cell debris, and 0.9 mL of the supernatant was transferred to a new tube. After a second spin at 20,000 g for 10 min, 0.8 mL of the supernatant was transferred to a new tube. Metabolites in the extraction buffer were dried using a vacuum concentrator system (Labconco) and stored at -80°C until analysis. Dried metabolite extracts were resuspended in 60% acetonitrile for injection. |
Combined analysis:
| Analysis ID | AN004186 | AN004187 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Shimadzu 20AD | Shimadzu 20AD |
| Column | Merck SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | Merck SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| MS Type | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole |
| MS instrument name | ABI Sciex 6500+ QTrap | ABI Sciex 6500+ QTrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak intensity | Peak intensity |
Chromatography:
| Chromatography ID: | CH003102 |
| Chromatography Summary: | Low pH polar |
| Instrument Name: | Shimadzu 20AD |
| Column Name: | Merck SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| Column Temperature: | 45 |
| Flow Gradient: | 0.01 min 80% B, 20 min 20% B, 20.5 min 80% B, 34 min 80% B. |
| Flow Rate: | 0.15ml/min |
| Solvent A: | 20 mM ammonium carbonate and 0.1% (v/v) ammonium hydroxide |
| Solvent B: | acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003933 |
| Analysis ID: | AN004186 |
| Instrument Name: | ABI Sciex 6500+ QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | SCIEX OS |
| Ion Mode: | POSITIVE |
| MS ID: | MS003934 |
| Analysis ID: | AN004187 |
| Instrument Name: | ABI Sciex 6500+ QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | SCIEX OS |
| Ion Mode: | NEGATIVE |
