Summary of Study ST001954

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 PR001241. The data can be accessed directly via it's Project DOI: 10.21228/M89996 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001954
Study TitleA pathogenic role for histone H3 copper reductase activity in a yeast model of Friedreich’s Ataxia
Study SummaryDisruptions to iron-sulfur (Fe-S) clusters, essential cofactors for a broad range of proteins, cause widespread cellular defects resulting in human disease. An underappreciated source of damage to Fe-S clusters are cuprous (Cu1+) ions. Since histone H3 enzymatically produces Cu1+ to support copper-dependent functions, we asked whether this activity could become detrimental to Fe-S clusters. Here, we report that histone H3-mediated Cu1+ toxicity is a major determinant of cellular functional pool of Fe-S clusters. Inadequate Fe-S cluster supply, either due to diminished assembly as occurs in Friedreich’s Ataxia or defective distribution, causes severe metabolic and growth defects in S. cerevisiae. Decreasing Cu1+ abundance, through attenuation of histone cupric reductase activity or depletion of total cellular copper, restored Fe-S cluster-dependent metabolism and growth. Our findings reveal a novel interplay between chromatin and mitochondria in Fe-S cluster homeostasis, and a potential pathogenic role for histone enzyme activity and Cu1+ in diseases with Fe-S cluster dysfunction.
Institute
University of California, Los Angeles
Last NameMatulionis
First NameNedas
Address615 Charles E Young Dr S, BSRB 354-05
Emailnmatulionis@mednet.ucla.edu
Phone3302346450
Submit Date2021-10-21
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2021-11-12
Release Version1
Nedas Matulionis Nedas Matulionis
https://dx.doi.org/10.21228/M89996
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001241
Project DOI:doi: 10.21228/M89996
Project Title:A pathogenic role for histone H3 copper reductase activity in a yeast model of Friedreich’s Ataxia
Project Summary:Disruptions to iron-sulfur (Fe-S) clusters, essential cofactors for a broad range of proteins, cause widespread cellular defects resulting in human disease. An underappreciated source of damage to Fe-S clusters are cuprous (Cu1+) ions. Since histone H3 enzymatically produces Cu1+ to support copper-dependent functions, we asked whether this activity could become detrimental to Fe-S clusters. Here, we report that histone H3-mediated Cu1+ toxicity is a major determinant of cellular functional pool of Fe-S clusters. Inadequate Fe-S cluster supply, either due to diminished assembly as occurs in Friedreich’s Ataxia or defective distribution, causes severe metabolic and growth defects in S. cerevisiae. Decreasing Cu1+ abundance, through attenuation of histone cupric reductase activity or depletion of total cellular copper, restored Fe-S cluster-dependent metabolism and growth. Our findings reveal a novel interplay between chromatin and mitochondria in Fe-S cluster homeostasis, and a potential pathogenic role for histone enzyme activity and Cu1+ in diseases with Fe-S cluster dysfunction.
Institute:University of California, Los Angeles
Department:Biomedical Sciences
Last Name:Matulionis
First Name:Nedas
Address:615 Charles E Young Dr S, BSRB 354-05
Email:nmatulionis@mednet.ucla.edu
Phone:3302346450

Subject:

Subject ID:SU002032
Subject Type:Yeast
Subject Species:Saccharomyces cerevisiae
Taxonomy ID:4932
Species Group:Yeast

Factors:

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

mb_sample_id local_sample_id Strain
SA184098cells-yeast-H3-dSGH1-01dGsh1
SA184099cells-yeast-H3-dSGH1-05dGsh1
SA184100cells-yeast-H3-dSGH1-03dGsh1
SA184101cells-yeast-H3-dSGH1-04dGsh1
SA184102cells-yeast-H3-dSGH1-02dGsh1
SA184088cells-yeast-H3-A110C-02H3A110C
SA184089cells-yeast-H3-A110C-05H3A110C
SA184090cells-yeast-H3-A110C-03H3A110C
SA184091cells-yeast-H3-A110C-04H3A110C
SA184092cells-yeast-H3-A110C-01H3A110C
SA184093cells-yeast-H3-H113N-05H3H113N
SA184094cells-yeast-H3-H113N-04H3H113N
SA184095cells-yeast-H3-H113N-03H3H113N
SA184096cells-yeast-H3-H113N-01H3H113N
SA184097cells-yeast-H3-H113N-02H3H113N
SA184103cells-yeast-WT-04wild type
SA184104cells-yeast-WT-01wild type
SA184105cells-yeast-WT-02wild type
SA184106cells-yeast-WT-05wild type
SA184107cells-yeast-WT-03wild type
Showing results 1 to 20 of 20

Collection:

Collection ID:CO002025
Collection Summary:Please refer to Treatment and Sample Prep sections.
Sample Type:Yeast cells

Treatment:

Treatment ID:TR002044
Treatment Summary:Yeast strains with wild type or mutant histone H3 were cultured in yeast Synthetic Complete Medium before collection and extraction. As a control and for comparison, a strain with GSH1 deleted is included. GSH1 encodes for gamma glutamylcysteine synthetase, which catalyzes the first step in glutathione biosynthesis.

Sample Preparation:

Sampleprep ID:SP002038
Sampleprep Summary:To extract metabolites, we washed the cells with ice-cold 150 mM ammonium acetate, pH 7.3, and then added 500 uL 80% methanol and incubated for 20 minutes at -80°C. Cells were then scraped off the plate, vortexed and centrifuged for 10 minutes at maximum speed. We dried 400 uL of the supernatant under vacuum and stored the dried metabolites at -80°C. Dried metabolites were reconstituted in 100 µL of a 50% acetonitrile(ACN) 50% dH20 solution. Samples were vortexed and spun down for 10 min at 17,000g. 70 µL of the supernatant was then transferred to HPLC glass vials.

Chromatography:

Chromatography ID:CH002351
Chromatography Summary:Samples were run on a Vanquish (Thermo Scientific) UHPLC system with mobile phase A (20 mM ammonium carbonate, pH 9.7) and mobile phase B (100% Acetonitrile) at a flow rate of 150 µL/min on a SeQuant ZIC-pHILIC Polymeric column (2.1 × 150 mm 5 μm, EMD Millipore) at 35°C. Separation was achieved with a linear gradient from 20% A to 80% A in 20 min followed by a linear gradient from 80% A to 20% A from 20 min to 20.5 min. 20% A was then held from 20.5 min to 28 min.
Instrument Name:Thermo Vanquish Horizon
Column Name:SeQuant ZIC-HILIC (150 x 2.1mm,5um)
Column Temperature:35°C
Flow Gradient:100% Acetonitrile
Flow Rate:150 µL/min
Internal Standard:10 nM Trifluoromethanesulfonate (extraction buffer)
Solvent A:100% water; 20 mM ammonium carbonate, pH 9.7
Solvent B:100% acetonitrile
Chromatography Type:HILIC

Analysis:

Analysis ID:AN003179
Laboratory Name:UCLA
Analysis Type:MS
Operator Name:Nedas Matulionis
Chromatography ID:CH002351
Num Factors:4
Num Metabolites:124
Units:Peak Area
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