Study Follows Proteome Consequences in Yeast Models Missing Individual Genes

A team at the Institute of Molecular Biology and other centers in Germany and the US consider the functional insights that can be gained by following protein shifts that stem from alterations affecting individual, nonessential genes across the genome in the yeast model organism Schizosaccharomyces pombe for a paper in Nature Communications. Using quantitative mass spec analyses, the researchers tracked proteomic profiles found in S. pombe knockout strains where 3,300 nonessential genes had been systematically and individually knocked out, using the resulting protein clusters to dig into the functions of the missing genes. "[W]e provide a comprehensive proteomics resource for the effect of single gene knockouts in a eukaryotic organism, surpassing any transcriptome screen in yeast to date," the authors note. "We used the protein expression data as a basis for functional annotation and selected 94 knockout strains to study posttranscriptional gene regulation to show that optimal codon usage is one possible scenario for the upregulation of protein expression under stable [messenger RNA] conditions.