Document Detail


High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection.
MedLine Citation:
PMID:  20610602     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The measurement of small molecule metabolites on a large scale offers the opportunity for a more complete understanding of cellular metabolism. We developed a high-throughput method to quantify primary amine-containing metabolites in the yeast Saccharomyces cerevisiae by the use of capillary electrophoresis in combination with fluorescent derivatization of cell extracts. We measured amino acid levels in the yeast deletion collection, a set of approximately 5000 strains each lacking a single gene, and developed a computational pipeline for data analysis. Amino acid peak assignments were validated by mass spectrometry, and the overall approach was validated by the result that expected pathway intermediates accumulate in mutants of the arginine biosynthetic pathway. Global analysis of the deletion collection was carried out using clustering methods. We grouped strains based on their metabolite profiles, revealing clusters of mutants enriched for genes encoding mitochondrial proteins, urea cycle enzymes, and vacuolar ATPase functions. One of the most striking profiles, common among several strains lacking ribosomal protein genes, accumulated lysine and a lysine-related metabolite. Mutations in the homologous ribosomal protein genes in the human result in Diamond-Blackfan anemia, demonstrating that metabolite data may have potential value in understanding disease pathology. This approach establishes metabolite profiling as capable of characterizing genes in a large collection of genetic variants.
Authors:
Sara J Cooper; Gregory L Finney; Shauna L Brown; Sven K Nelson; Jay Hesselberth; Michael J MacCoss; Stanley Fields
Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't     Date:  2010-07-07
Journal Detail:
Title:  Genome research     Volume:  20     ISSN:  1549-5469     ISO Abbreviation:  Genome Res.     Publication Date:  2010 Sep 
Date Detail:
Created Date:  2010-09-02     Completed Date:  2010-12-23     Revised Date:  2011-07-25    
Medline Journal Info:
Nlm Unique ID:  9518021     Medline TA:  Genome Res     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1288-96     Citation Subset:  IM    
Affiliation:
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
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MeSH Terms
Descriptor/Qualifier:
Amino Acids / analysis*,  chemistry,  metabolism
Gene Deletion
Gene Expression Regulation, Fungal
Genetic Variation
Metabolomics / methods*
Saccharomyces cerevisiae / genetics*,  metabolism
Saccharomyces cerevisiae Proteins / genetics
Grant Support
ID/Acronym/Agency:
F32 DK080608/DK/NIDDK NIH HHS; P41 RR11823/RR/NCRR NIH HHS; //Howard Hughes Medical Institute
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Saccharomyces cerevisiae Proteins
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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