Summary of Study ST001901

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 PR001196. The data can be accessed directly via it's Project DOI: 10.21228/M83X4N 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 IDST001901
Study TitleMitochondrial-Derived Compartments Facilitate Cellular Adaptation to Amino Acid Stress
Study SummaryAmino acids are essential building blocks of life. However, increasing evidence suggests that elevated amino acids cause cellular toxicity associated with numerous metabolic disorders. How cells cope with elevated amino acids remains poorly understood. Here, we show that a previously identified cellular structure, the mitochondrial-derived compartment (MDC), functions to protect cells from amino acid stress. In response to amino acid elevation, MDCs are generated from mitochondria, where they selectively sequester and deplete SLC25A nutrient carriers and their associated import receptor Tom70 from the organelle. Generation of MDCs promotes amino acid catabolism, and their formation occurs simultaneously with transporter removal at the plasma membrane via the multi-vesicular body (MVB) pathway. Combined loss of vacuolar amino acid storage, MVBs and MDCs renders cells sensitive to high amino acid stress. Thus, we propose that MDCs operate as part of a coordinated cell network that facilitates amino acid homoeostasis through post-translational nutrient transporter remodeling.
Institute
University of Utah School of Medicine
DepartmentBiochemistry
LaboratoryHughes Lab
Last NameHughes
First NameAdam
Address15 N Medical Drive East, RM 4100, Salt Lake City, UT, 84112, USA
Emailhughes@biochem.utah.edu
Phone8015812481
Submit Date2021-07-22
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2021-08-25
Release Version1
Adam Hughes Adam Hughes
https://dx.doi.org/10.21228/M83X4N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001196
Project DOI:doi: 10.21228/M83X4N
Project Title:Mitochondrial-Derived Compartments Facilitate Cellular Adaptation to Amino Acid Stress
Project Summary:Amino acids are essential building blocks of life. However, increasing evidence suggests that elevated amino acids cause cellular toxicity associated with numerous metabolic disorders. How cells cope with elevated amino acids remains poorly understood. Here, we show that a previously identified cellular structure, the mitochondrial-derived compartment (MDC), functions to protect cells from amino acid stress. In response to amino acid elevation, MDCs are generated from mitochondria, where they selectively sequester and deplete SLC25A nutrient carriers and their associated import receptor Tom70 from the organelle. Generation of MDCs promotes amino acid catabolism, and their formation occurs simultaneously with transporter removal at the plasma membrane via the multi-vesicular body (MVB) pathway. Combined loss of vacuolar amino acid storage, MVBs and MDCs renders cells sensitive to high amino acid stress. Thus, we propose that MDCs operate as part of a coordinated cell network that facilitates amino acid homoeostasis through post-translational nutrient transporter remodeling.
Institute:University of Utah School of Medicine
Department:Biochemistry
Laboratory:Hughes Lab
Last Name:Hughes
First Name:Adam
Address:15 N Medical Drive East, RM 4100, Salt Lake City, UT, 84112, USA
Email:hughes@biochem.utah.edu
Phone:8015812481

Subject:

Subject ID:SU001979
Subject Type:Yeast
Subject Species:Saccharomyces cerevisiae
Taxonomy ID:4932

Factors:

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

mb_sample_id local_sample_id Genotype Media Treatment
SA176249Hughes_Schuler_20200818_7200_20to1_Yeast_6Agem1 knockout SD+Leucine ConcA
SA176250Hughes_Schuler_20200818_7200_20to1_Yeast_6Dgem1 knockout SD+Leucine ConcA
SA176251Hughes_Schuler_20200818_7200_20to1_Yeast_6Bgem1 knockout SD+Leucine ConcA
SA176252Hughes_Schuler_20200818_7200_20to1_Yeast_6Cgem1 knockout SD+Leucine ConcA
SA176253Hughes_Schuler_20200818_7200_20to1_Yeast_2Dgem1 knockout SD+Leucine DMSO
SA176254Hughes_Schuler_20200818_7200_20to1_Yeast_2Cgem1 knockout SD+Leucine DMSO
SA176255Hughes_Schuler_20200818_7200_20to1_Yeast_2Bgem1 knockout SD+Leucine DMSO
SA176256Hughes_Schuler_20200818_7200_20to1_Yeast_2Agem1 knockout SD+Leucine DMSO
SA176257Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_5agem1 knockout YPAD ConcA
SA176258Hughes_Schuler_20200825_7200_20to1_MSTFA_11gem1 knockout YPAD ConcA
SA176259Hughes_Schuler_20200825_7200_20to1_MSTFA_17gem1 knockout YPAD ConcA
SA176260Hughes_Schuler_20200825_7200_20to1_MSTFA_5gem1 knockout YPAD ConcA
SA176261Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_23gem1 knockout YPAD ConcA
SA176262Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_11gem1 knockout YPAD ConcA
SA176263Hughes_Schuler_20200825_7200_20to1_MSTFA_23gem1 knockout YPAD ConcA
SA176264Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_17gem1 knockout YPAD ConcA
SA176265Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_22gem1 knockout YPAD DMSO
SA176266Hughes_Schuler_20200825_7200_20to1_MSTFA_16gem1 knockout YPAD DMSO
SA176267Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_16gem1 knockout YPAD DMSO
SA176268Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_10gem1 knockout YPAD DMSO
SA176269Hughes_Schuler_20200825_7200_20to1_MSTFA_22gem1 knockout YPAD DMSO
SA176270Hughes_Schuler_20200825_7200_20to1_MSTFA_4gem1 knockout YPAD DMSO
SA176271Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_4gem1 knockout YPAD DMSO
SA176272Hughes_Schuler_20200825_7200_20to1_MSTFA_10gem1 knockout YPAD DMSO
SA176273Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_18gem1 knockout YPAD Rap
SA176274Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_12gem1 knockout YPAD Rap
SA176275Hughes_Schuler_20200825_7200_20to1_MSTFA_6gem1 knockout YPAD Rap
SA176276Hughes_Schuler_20200825_7200_20to1_MSTFA_24gem1 knockout YPAD Rap
SA176277Hughes_Schuler_20200825_7200_20to1_MSTFA_18gem1 knockout YPAD Rap
SA176278Hughes_Schuler_20200825_7200_20to1_MSTFA_12gem1 knockout YPAD Rap
SA176279Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_24gem1 knockout YPAD Rap
SA176280Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_5gem1 knockout YPAD Rap
SA176281Hughes_Schuler_20200818_7200_20to1_Yeast_8Agem1 vps27 double knockout SD+Leucine ConcA
SA176282Hughes_Schuler_20200818_7200_20to1_Yeast_8Dgem1 vps27 double knockout SD+Leucine ConcA
SA176283Hughes_Schuler_20200818_7200_20to1_Yeast_4Dgem1 vps27 double knockout SD+Leucine ConcA
SA176284Hughes_Schuler_20200818_7200_20to1_Yeast_8Bgem1 vps27 double knockout SD+Leucine ConcA
SA176285Hughes_Schuler_20200818_7200_20to1_Yeast_8Cgem1 vps27 double knockout SD+Leucine ConcA
SA176286Hughes_Schuler_20200818_7200_20to1_Yeast_4Cgem1 vps27 double knockout SD+Leucine DMSO
SA176287Hughes_Schuler_20200818_7200_20to1_Yeast_4Bgem1 vps27 double knockout SD+Leucine DMSO
SA176288Hughes_Schuler_20200818_7200_20to1_Yeast_4Agem1 vps27 double knockout SD+Leucine DMSO
SA176218Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_QC2Pooled QC sample N/A N/A
SA176219Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_QC1Pooled QC sample N/A N/A
SA176220Hughes_Schuler_20200825_7200_20to1_MSTFA_QC3Pooled QC sample N/A N/A
SA176221Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_QC3Pooled QC sample N/A N/A
SA176222Hughes_Schuler_20200825_7200_20to1_MSTFA_QC2Pooled QC sample N/A N/A
SA176223Hughes_Schuler_20200818_7200_20to1_Yeast_QC4Pooled QC sample N/A N/A
SA176224Hughes_Schuler_20200818_7200_20to1_Yeast_QC1Pooled QC sample N/A N/A
SA176225Hughes_Schuler_20200818_7200_20to1_Yeast_QC2Pooled QC sample N/A N/A
SA176226Hughes_Schuler_20200818_7200_20to1_Yeast_QC3Pooled QC sample N/A N/A
SA176227Hughes_Schuler_20200825_7200_20to1_MSTFA_QC4Pooled QC sample N/A N/A
SA176228Hughes_Schuler_20200825_7200_20to1_MSTFA_QC1Pooled QC sample N/A N/A
SA176229Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_QC4Pooled QC sample N/A N/A
SA176230Hughes_Schuler_20190522_5977b_10to1_Yeast_QC6Pooled QC sample N/A N/A
SA176231Hughes_Schuler_20190522_5977b_10to1_Yeast_QC5Pooled QC sample N/A N/A
SA176232Hughes_Schuler_20190522_5977b_10to1_Yeast_QC8Pooled QC sample N/A N/A
SA176233Hughes_Schuler_20190522_5977b_10to1_Yeast_QC7Pooled QC sample N/A N/A
SA176234Hughes_Schuler_20200825_7200_20to1_MSTFA_PB1Process blank N/A N/A
SA176235Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_PB3Process blank N/A N/A
SA176236Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_PB4Process blank N/A N/A
SA176237Hughes_Schuler_20200818_7200_20to1_Yeast_PB1Process blank N/A N/A
SA176238Hughes_Schuler_20200825_7200_20to1_MSTFA_PB2Process blank N/A N/A
SA176239Hughes_Schuler_20200825_7200_20to1_MSTFA_PB3Process blank N/A N/A
SA176240Hughes_Schuler_20200825_7200_20to1_MSTFA_PB4Process blank N/A N/A
SA176241Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_PB2Process blank N/A N/A
SA176242Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_PB1Process blank N/A N/A
SA176243Hughes_Schuler_20200818_7200_20to1_Yeast_PB4Process blank N/A N/A
SA176244Hughes_Schuler_20200818_7200_20to1_Yeast_PB3Process blank N/A N/A
SA176245Hughes_Schuler_20200818_7200_20to1_Yeast_PB2Process blank N/A N/A
SA176246Hughes_Schuler_20190522_5977b_10to1_Yeast_PB4Process blank N/A N/A
SA176247Hughes_Schuler_20190522_5977b_10to1_Yeast_PB5Process blank N/A N/A
SA176248Hughes_Schuler_20190522_5977b_10to1_Yeast_PB6Process blank N/A N/A
SA176289Hughes_Schuler_20200818_7200_20to1_Yeast_7Dvps27 knockout SD+Leucine ConcA
SA176290Hughes_Schuler_20200818_7200_20to1_Yeast_7Cvps27 knockout SD+Leucine ConcA
SA176291Hughes_Schuler_20200818_7200_20to1_Yeast_7Bvps27 knockout SD+Leucine ConcA
SA176292Hughes_Schuler_20200818_7200_20to1_Yeast_7Avps27 knockout SD+Leucine ConcA
SA176293Hughes_Schuler_20200818_7200_20to1_Yeast_3Avps27 knockout SD+Leucine DMSO
SA176294Hughes_Schuler_20200818_7200_20to1_Yeast_3Bvps27 knockout SD+Leucine DMSO
SA176295Hughes_Schuler_20200818_7200_20to1_Yeast_3Cvps27 knockout SD+Leucine DMSO
SA176296Hughes_Schuler_20200818_7200_20to1_Yeast_3Dvps27 knockout SD+Leucine DMSO
SA176297Hughes_Schuler_20190522_5977b_10to1_Yeast_34wild-type MinD DMSO
SA176298Hughes_Schuler_20190522_5977b_10to1_Yeast_52wild-type MinD DMSO
SA176299Hughes_Schuler_20190522_5977b_10to1_Yeast_43wild-type MinD DMSO
SA176300Hughes_Schuler_20200818_7200_20to1_Yeast_5Awild-type SD+Leucine ConcA
SA176301Hughes_Schuler_20200818_7200_20to1_Yeast_5Cwild-type SD+Leucine ConcA
SA176302Hughes_Schuler_20200818_7200_20to1_Yeast_5Bwild-type SD+Leucine ConcA
SA176303Hughes_Schuler_20200818_7200_20to1_Yeast_5Dwild-type SD+Leucine ConcA
SA176304Hughes_Schuler_20200818_7200_20to1_Yeast_1Cwild-type SD+Leucine DMSO
SA176305Hughes_Schuler_20200818_7200_20to1_Yeast_1Awild-type SD+Leucine DMSO
SA176306Hughes_Schuler_20200818_7200_20to1_Yeast_1Bwild-type SD+Leucine DMSO
SA176307Hughes_Schuler_20200818_7200_20to1_Yeast_1Dwild-type SD+Leucine DMSO
SA176308Hughes_Schuler_20190522_5977b_10to1_Yeast_31wild-type SD DMSO
SA176309Hughes_Schuler_20190522_5977b_10to1_Yeast_40wild-type SD DMSO
SA176310Hughes_Schuler_20190522_5977b_10to1_Yeast_49wild-type SD DMSO
SA176311Hughes_Schuler_20200825_7200_20to1_MSTFA_20wild-type YPAD ConcA
SA176312Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_14wild-type YPAD ConcA
SA176313Hughes_Schuler_20200825_7200_20to1_MSTFA_14wild-type YPAD ConcA
SA176314Hughes_Schuler_20200825_7200_20to1_MSTFA_8wild-type YPAD ConcA
SA176315Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_8wild-type YPAD ConcA
SA176316Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_20wild-type YPAD ConcA
SA176317Hughes_Schuler_20200807_MSTFA_5977b_20to1_SC_2wild-type YPAD ConcA
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Collection:

Collection ID:CO001972
Collection Summary:See STAR methods file
Collection Protocol Filename:STAR_methods.pdf
Sample Type:Yeast cells

Treatment:

Treatment ID:TR001991
Treatment Summary:See STAR Methods file
Treatment Protocol Filename:STAR_methods.pdf

Sample Preparation:

Sampleprep ID:SP001985
Sampleprep Summary:See STAR Methods file
Sampleprep Protocol Filename:STAR_methods.pdf

Combined analysis:

Analysis ID AN003089 AN003090 AN003091 AN003092
Analysis type MS MS MS MS
Chromatography type GC GC GC GC
Chromatography system Agilent 5977B Agilent 7200 Agilent 7200 Agilent 5977B
Column Phenomenex Zebron ZB-WAXplus (30m x 0.25mm, 0.25um) Phenomenex Zebron ZB-WAXplus (30m x 0.25mm, 0.25um) Phenomenex Zebron ZB-WAXplus (30m x 0.25mm, 0.25um) Phenomenex Zebron ZB-WAXplus (30m x 0.25mm, 0.25um)
MS Type EI EI EI EI
MS instrument type Single quadrupole QTOF QTOF Single quadrupole
MS instrument name Agilent 5977B Agilent 7200 Agilent 7200 Agilent 5977B
Ion Mode POSITIVE POSITIVE POSITIVE POSITIVE
Units area under the curve area under the curve area under the curve area under the curve

Chromatography:

Chromatography ID:CH002280
Instrument Name:Agilent 5977B
Column Name:Phenomenex Zebron ZB-WAXplus (30m x 0.25mm, 0.25um)
Chromatography Type:GC
  
Chromatography ID:CH002281
Instrument Name:Agilent 7200
Column Name:Phenomenex Zebron ZB-WAXplus (30m x 0.25mm, 0.25um)
Chromatography Type:GC
  
Chromatography ID:CH002282
Instrument Name:Agilent 7200
Column Name:Phenomenex Zebron ZB-WAXplus (30m x 0.25mm, 0.25um)
Chromatography Type:GC
  
Chromatography ID:CH002283
Instrument Name:Agilent 5977B
Column Name:Phenomenex Zebron ZB-WAXplus (30m x 0.25mm, 0.25um)
Chromatography Type:GC

MS:

MS ID:MS002871
Analysis ID:AN003089
Instrument Name:Agilent 5977B
Instrument Type:Single quadrupole
MS Type:EI
MS Comments:N/A
Ion Mode:POSITIVE
  
MS ID:MS002872
Analysis ID:AN003090
Instrument Name:Agilent 7200
Instrument Type:QTOF
MS Type:EI
MS Comments:N/A
Ion Mode:POSITIVE
  
MS ID:MS002873
Analysis ID:AN003091
Instrument Name:Agilent 7200
Instrument Type:QTOF
MS Type:EI
MS Comments:N/A
Ion Mode:POSITIVE
  
MS ID:MS002874
Analysis ID:AN003092
Instrument Name:Agilent 5977B
Instrument Type:Single quadrupole
MS Type:EI
MS Comments:N/A
Ion Mode:POSITIVE
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