Summary of Study ST002542

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.

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Study IDST002542
Study TitleMethionine restriction constrains lipoylation and activates mitochondria for nitrogenic synthesis of amino acids (Part 2)
Study SummaryMethionine 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
Life Sciences Institute, ZheJiang University
Last NameCunqi
First NameYe
Address866 Yuhangtang Rd, Hangzhou 310058, P.R. China
Emailyecunqi@zju.edu.cn
Phone15267181160
Submit Date2023-04-05
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2023-04-21
Release Version1
Ye Cunqi Ye Cunqi
https://dx.doi.org/10.21228/M83M7P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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:Life Sciences Institute, ZheJiang University
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:SU002642
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 label
SA255575S1S2 0h_10h
SA255576S1S2 0h _30h
SA255577S1S2 0h_20h
SA255578S1S2 15h_115h
SA255579S1S2 15h_315h
SA255580S1S2 15h_215h
SA255581S1S2 15h_1+15h+
SA255582S1S2 15h_3+15h+
SA255583S1S2 15h_2+15h+
SA255584S1S2 2h_22h
SA255585S1S2 2h_32h
SA255586S1S2 2h_12h
SA255587S1S2 2h_3+2h+
SA255588S1S2 2h_1+2h+
SA255589S1S2 2h_2+2h+
SA255590S1S2 4h_24h
SA255591S1S2 4h_34h
SA255592S1S2 4h_14h
SA255593S1S2 4h_3+4h+
SA255594S1S2 4h_2+4h+
SA255595S1S2 4h_1+4h+
SA255596S1S2 6h_36h
SA255597S1S2 6h_26h
SA255598S1S2 6h_16h
SA255599S1S2 6h_3+6h+
SA255600S1S2 6h_1+6h+
SA255601S1S2 6h_2+6h+
Showing results 1 to 27 of 27

Collection:

Collection ID:CO002635
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:TR002654
Treatment Summary:Mutant SAM1SAM2 DKO cells were cultured in SD medium with the supplements of SAM and growed to log phase, then cells were washed with normal SD medium and re-cultured in SD medium

Sample Preparation:

Sampleprep ID:SP002648
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 AN004188 AN004189
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 QTRAP QTRAP
MS instrument name ABI Sciex 6500+ ABI Sciex 6500+
Ion Mode POSITIVE NEGATIVE
Units Peak intensity Peak intensity

Chromatography:

Chromatography ID:CH003103
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:MS003935
Analysis ID:AN004188
Instrument Name:ABI Sciex 6500+
Instrument Type:QTRAP
MS Type:ESI
MS Comments:SCIEX OS
Ion Mode:POSITIVE
  
MS ID:MS003936
Analysis ID:AN004189
Instrument Name:ABI Sciex 6500+
Instrument Type:QTRAP
MS Type:ESI
MS Comments:SCIEX OS
Ion Mode:NEGATIVE
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