Cooper SJ~Fields S, 2010

Pubmed ID 20610602
Title High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection.
Authors Sara J Cooper, Gregory L Finney, Shauna L Brown, Sven K Nelson, Jay Hesselberth, Michael J MacCoss, Stanley Fields
Abstract 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.
Citation Genome Res. 2010; 20:1288-96

Datasets

Download the list of datasets
Paper Phenotype Condition Reference Collection Tested mutants Data Details
Cooper SJ~Fields S, 2010 abundance of a lysin-related metabolite minimal complete [standard] hap a 2,021 Quantitative
Cooper SJ~Fields S, 2010 abundance of arginine minimal complete [standard] hap a 4,305 Quantitative
Cooper SJ~Fields S, 2010 abundance of biotin minimal complete [standard] hap a 2,853 Quantitative
Cooper SJ~Fields S, 2010 abundance of N-acetyl ornithine minimal complete [standard] hap a 3,318 Quantitative
Cooper SJ~Fields S, 2010 abundance of leucine + isoleucine + citrulline minimal complete [standard] hap a 4,306 Quantitative
Cooper SJ~Fields S, 2010 abundance of glutamine + valine minimal complete [standard] hap a 4,310 Quantitative
Cooper SJ~Fields S, 2010 abundance of methionine + proline minimal complete [standard] hap a 4,297 Quantitative
Cooper SJ~Fields S, 2010 abundance of threonine minimal complete [standard] hap a 3,980 Quantitative
Cooper SJ~Fields S, 2010 abundance of alanine minimal complete [standard] hap a 4,309 Quantitative
Cooper SJ~Fields S, 2010 abundance of serine minimal complete [standard] hap a 3,999 Quantitative
Cooper SJ~Fields S, 2010 abundance of asparagine + tyrosine minimal complete [standard] hap a 4,304 Quantitative
Cooper SJ~Fields S, 2010 abundance of glycine minimal complete [standard] hap a 4,305 Quantitative
Cooper SJ~Fields S, 2010 abundance of lysine minimal complete [standard] hap a 4,309 Quantitative
Cooper SJ~Fields S, 2010 abundance of ornithine minimal complete [standard] hap a 4,031 Quantitative
Cooper SJ~Fields S, 2010 abundance of glutamate minimal complete [standard] hap a 4,276 Quantitative
Cooper SJ~Fields S, 2010 abundance of aspartic acid minimal complete [standard] hap a 3,963 Quantitative

Curation history

Tested strains

Jan. 22, 2014 Loaded.

Data

Jan. 22, 2014 Loaded.
May 7, 2014 Clarification needed.
May 7, 2014 Request sent.
May 8, 2014 Loaded.