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

Curation history

Data

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

Tested strains

Jan. 22, 2014 Loaded.