Summary of Study ST003854

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 PR002411. The data can be accessed directly via it's Project DOI: 10.21228/M80C12 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.

Show all samples  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST003854
Study TitleLaboratory evolutions lead to reproducible mutations in PDR3 conferring resistance to MCHM
Study TypeLCMS untargeted analysis
Study Summary4-methylcyclohexane methanol (MCHM), an alicyclic alcohol, is a synthetic hydrotrope that induces a starvation response by upregulation of biosynthetic pathways despite the availability of nutrients. To investigate how cellular metabolism can tolerate MCHM, we evolved eight MHCM-resistant strains of S. cerevisiae. To map the SNPs, we resequenced the YJM789 genome with PacBio. We identified thousands of SNPs and indel variants per strain, which was a consistent number between strains that evolved resistance and control strains that remained sensitive. One gene was mutated in all resistant strains. PDR3, controls transcription for the pleiotropic drug response and is the most significant driver of adaptive MCHM resistance in yeast. While many of the evolved alleles of PDR3 would likely produce functional proteins, a knockout in the parent YJM789 strain was sufficient to produce resistance to MCHM. The pdr3 resistance is mediated through Med15, a component of the Mediator complex which regulates activation by transcription factors of RNA Pol II. Pdr3 can homodimerize or dimerize with Pdr1, another transcription factor and loss of Pdr1 also confers MCHM resistance. Normal catabolism of amino acids uses the Pleiotropic Drug Response (PDR) pathway to export breakdown products and loss of pdr3 altered the glutathione and its intermediates. While low levels of ROS are induced by MCHM excess levels of most nitrogen sources rescued MCHM growth. Mutations in PDR3 are first known to increase resistance to this novel hydrotropic chemical.
Institute
West Virginia University
DepartmentBiology
LaboratoryGallagher Lab
Last NamePatriarcheas
First NameDionysios
AddressPO Box 6057, Morgantown, West Virginia, 26506, USA
Emaildp00034@mix.wvu.edu
Phone3046851480
Submit Date2025-02-25
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-04-23
Release Version1
Dionysios Patriarcheas Dionysios Patriarcheas
https://dx.doi.org/10.21228/M80C12
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002411
Project DOI:doi: 10.21228/M80C12
Project Title:Laboratory evolutions lead to reproducible mutations in PDR3 conferring resistance to MCHM
Project Type:LCMS untargeted analysis
Project Summary:4-methylcyclohexane methanol (MCHM), an alicyclic alcohol, is a synthetic hydrotrope that induces a starvation response by upregulation of biosynthetic pathways despite the availability of nutrients. To investigate how cellular metabolism can tolerate MCHM, we evolved eight MHCM-resistant strains of S. cerevisiae. To map the SNPs, we resequenced the YJM789 genome with PacBio. We identified thousands of SNPs and indel variants per strain, which was a consistent number between strains that evolved resistance and control strains that remained sensitive. One gene was mutated in all resistant strains. PDR3, controls transcription for the pleiotropic drug response and is the most significant driver of adaptive MCHM resistance in yeast. While many of the evolved alleles of PDR3 would likely produce functional proteins, a knockout in the parent YJM789 strain was sufficient to produce resistance to MCHM. The pdr3 resistance is mediated through Med15, a component of the Mediator complex which regulates activation by transcription factors of RNA Pol II. Pdr3 can homodimerize or dimerize with Pdr1, another transcription factor and loss of Pdr1 also confers MCHM resistance. Normal catabolism of amino acids uses the Pleiotropic Drug Response (PDR) pathway to export breakdown products and loss of pdr3 altered the glutathione and its intermediates. While low levels of ROS are induced by MCHM excess levels of most nitrogen sources rescued MCHM growth. Mutations in PDR3 are first known to increase resistance to this novel hydrotropic chemical.
Institute:West Virginia University
Department:Biology
Laboratory:Gallagher Lab
Last Name:Patriarcheas
First Name:Dionysios
Address:PO Box 6057, Morgantown, West Virginia, 26506, USA
Email:dp00034@mix.wvu.edu
Phone:3046851480
Funding Source:-
Project Comments:-
Publications:Laboratory evolutions lead to reproducible mutations in PDR3 conferring resistance to MCHM

Subject:

Subject ID:SU003988
Subject Type:Yeast
Subject Species:Saccharomyces cerevisiae
Taxonomy ID:4932
Genotype Strain:YJM789

Factors:

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

mb_sample_id local_sample_id Sample Strain
SA422037PDR3_Control2PDR3Control PDR3_KO
SA422038PDR3_Control1PDR3Control PDR3_KO
SA422039PDR3_Control4PDR3Control PDR3_KO
SA422040PDR3_Control3PDR3Control PDR3_KO
SA422041PDR3_MCHM1PDR3MCHM PDR3_KO
SA422042PDR3_MCHM2PDR3MCHM PDR3_KO
SA422043PDR3_MCHM3PDR3MCHM PDR3_KO
SA422044PDR3_MCHM4PDR3MCHM PDR3_KO
SA422045YJM789_Control2YJM789Control Wildtype
SA422046YJM789_Control3YJM789Control Wildtype
SA422047YJM789_Control4YJM789Control Wildtype
SA422048YJM789_Control1YJM789Control Wildtype
SA422049YJM789_MCHM1YJM789MCHM Wildtype
SA422050YJM789_MCHM2YJM789MCHM Wildtype
SA422051YJM789_MCHM3YJM789MCHM Wildtype
SA422052YJM789_MCHM4YJM789MCHM Wildtype
Showing results 1 to 16 of 16

Collection:

Collection ID:CO003981
Collection Summary:Metabolites were extracted via a cold methanol acetonitrile extraction from 2 OD unites of mid-logarithmic phase cells.
Sample Type:Culture Media

Treatment:

Treatment ID:TR003997
Treatment Summary:Untreated cells were harvested in mid logarithmic phase. Treated cells were exposed to 650 ppm of MCHM for 30 minutes.

Sample Preparation:

Sampleprep ID:SP003994
Sampleprep Summary:Liquid cell cultures were grown to mid-logarithmic phase and were subsequently exposed to 30 mins of MCHM treatment at 650 ppm. Cells were quenched in cold methanol and metabolites were extracted with a methanol-acetonitrile extraction protocol as described in Crutchfield et al 2010 (https://www.sciencedirect.com/science/article/pii/S0076687910700161).

Chromatography:

Chromatography ID:CH004803
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC BEH Amide (50 x 2.1 mm, 1.7 μm)
Column Temperature:40°C
Flow Gradient:The gradient started at 95% acetonitrile with 0.1% formic acid for 3 minutes at a flow rate of 1.2 mL/min, remained at 45% acetonitrile until minute 3.5, and then returned to 95% acetonitrile at minute 3.6 until minute 5.
Flow Rate:1.2 mL/min
Solvent A:100% Water
Solvent B:100% Acetonitrile; 0.1% Formic acid
Chromatography Type:HILIC

Analysis:

Analysis ID:AN006332
Analysis Type:MS
Chromatography ID:CH004803
Has Mz:1
Has Rt:1
Rt Units:Seconds
Results File:ST003854_AN006332_Results.txt
Units:Intensity
  logo