Summary of Study ST002397

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 PR001544. The data can be accessed directly via it's Project DOI: 10.21228/M8440H 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	ST002397
Study Title	System-level analysis of flux regulation of yeast show that glycolytic flux is controlled by allosteric regulation and enzyme phosphorylation
Study Summary	Energy metabolism is central for cellular function and has therefore evolved to be tightly regulated such that energy production can be balanced to energy demand. Energy is being produced in the central carbon metabolism (CCM) and even though there has been extensive studies on how fluxes through the different pathways in this part of metabolism are regulated. There is little understanding of how fluxes are affected by posttranslational modifications and by allosteric regulators. Here we integrated multi-omics data (intracellular metabolome, extracellular metabolome, proteome, phosphoproteome, and fluxome) under 9 different chemostat conditions for building a mathematical model that could map functional regulatory events (FREs) in the Saccharomyces cerevisiae. Using hierarchical analysis combined with the mathematical model, we observed pathway and metabolism-specific flux regulation mechanisms in the CCM. We also found that the glycolytic flux increased with specific growth rate, and this increase was accompanied by a decrease of both metabolites derived FREs and protein phosphorylation level.
Institute	Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University
Last Name	Chen
First Name	Min
Address	State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology
Email	mchen531@163.com
Phone	18582480786
Submit Date	2022-08-14
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2022-12-30
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001544
Project DOI:	doi: 10.21228/M8440H
Project Title:	Quantify the absolute abundace of metabolite
Project Summary:	Quantify the absolute abundace of metabolite of yeast under different specific growth rate.
Institute:	Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University
Last Name:	Chen
First Name:	Min
Address:	State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology
Email:	mchen531@163.com
Phone:	18582480786

Subject:

Subject ID:	SU002486
Subject Type:	Yeast
Subject Species:	Saccharomyces cerevisiae
Taxonomy ID:	4932
Gender:	Not applicable

Factors:

Subject type: Yeast; Subject species: Saccharomyces cerevisiae (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA239031	u0.027_pool1_PS	Control
SA239032	u0.355_pool1_PS	Glucose
SA239033	u0.385_pool1_PS	Glucose
SA239034	u0.316_pool1_PS	Glucose
SA239035	u0.207_pool1_PS	Glucose
SA239036	u0.051_pool1_PS	Glucose
SA239037	u0.118_pool1_PS	Glucose
SA239038	u0.154_pool1_PS	Glucose
SA239039	u0.249_pool1_PS	Glucose

Showing results 1 to 9 of 9

Showing results 1 to 9 of 9

Collection:

Collection ID:	CO002479
Collection Summary:	Cells were washed with cold PBS and them flash-frozen in liquid N2
Sample Type:	Yeast cells
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR002498
Treatment Summary:	For quantification of intracellular metabolite concentrations,1.0 mL-broth samples were rapidly withdrawn and quenched in pre-weighed tubes containing 5 mL cold (−40 °C) pure methanol followed immediately by vigorous vortexing. The quenched samples were rapidly weighed and poured into a filtration device containing a cellulose membrane and previously layered with 15 mL of cold methanol (−40 °C). Subsequently, a vacuum was applied followed by an immediate additional washing step with 15 mL cold methanol (−40 °C). The filter containing the cold washed biomass was then transferred into a 50 mL-falcon tube containing 30 mL of preheated (75 °C) aqueous ethanol solution (75% v/v). 100 μL of 13C cell extract was added to the tube as an internal standard. The tube containing the sample was then tightly closed, shaken vigorously, and placed into a water bath at 95 °C during 3 min for metabolite extraction. The tubes were then cooled using an ice bath and the filter was removed. This extract was then concentrated by complete evaporation of the ethanol–water mixture under vacuum, and resuspended in 500 μL milliQ water. After a first centrifugation at 15000 g for 5 min at 1 °C, the supernatant was transferred into a centrifugal filter unit and centrifuged again at the same conditions. The filtrate was placed into a screw-capped polypropylene vial and stored at −80 °C until further analysis. Samples were analyzed by LC-MS.

Treatment ID:

TR002498

Treatment Summary:

For quantification of intracellular metabolite concentrations,1.0 mL-broth samples were rapidly withdrawn and quenched in pre-weighed tubes containing 5 mL cold (−40 °C) pure methanol followed immediately by vigorous vortexing. The quenched samples were rapidly weighed and poured into a filtration device containing a cellulose membrane and previously layered with 15 mL of cold methanol (−40 °C). Subsequently, a vacuum was applied followed by an immediate additional washing step with 15 mL cold methanol (−40 °C). The filter containing the cold washed biomass was then transferred into a 50 mL-falcon tube containing 30 mL of preheated (75 °C) aqueous ethanol solution (75% v/v). 100 μL of 13C cell extract was added to the tube as an internal standard. The tube containing the sample was then tightly closed, shaken vigorously, and placed into a water bath at 95 °C during 3 min for metabolite extraction. The tubes were then cooled using an ice bath and the filter was removed. This extract was then concentrated by complete evaporation of the ethanol–water mixture under vacuum, and resuspended in 500 μL milliQ water. After a first centrifugation at 15000 g for 5 min at 1 °C, the supernatant was transferred into a centrifugal filter unit and centrifuged again at the same conditions. The filtrate was placed into a screw-capped polypropylene vial and stored at −80 °C until further analysis. Samples were analyzed by LC-MS.

Sample Preparation:

Sampleprep ID:	SP002492
Sampleprep Summary:	Total liquids are divided into liquid phase vials.
Processing Storage Conditions:	4℃
Extract Storage:	On ice

Combined analysis:

Analysis ID	AN003904
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Waters NanoAcquity
Column	Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type	ESI
MS instrument type	Triple quadrupole
MS instrument name	Thermo TSQ Quantum Ultra
Ion Mode	NEGATIVE
Units	umol/l

Chromatography:

Chromatography ID:	CH002890
Instrument Name:	Waters NanoAcquity
Column Name:	Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:	40
Flow Rate:	0.2ml/min
Solvent A:	100% water; 5 mM ammonium formate
Solvent B:	85% acetonitrile/15% water
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003643
Analysis ID:	AN003904
Instrument Name:	Thermo TSQ Quantum Ultra
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	Xcalibur
Ion Mode:	NEGATIVE