Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways

Abstract

Protein phosphorylation is a widespread posttranslational modification that regulates almost all cellular functions. To investigate the large number of phosphorylation events with unknown functions, we monitored the concentrations of several hundred intracellular metabolites in Saccharomyces cerevisiae yeast strains with deletions of 118 kinases or phosphatases. Whereas most deletion strains had no detectable difference in growth compared to wild-type yeast, two-thirds of deletion strains had alterations in metabolic profiles. For about half of the kinases and phosphatases encoded by the deleted genes, we inferred specific regulatory roles on the basis of knowledge about the affected metabolic pathways. We demonstrated that the phosphatase Ppq1 was required for metal homeostasis. Combining metabolomic data with published phosphoproteomic data in a stoichiometric model enabled us to predict functions for phosphorylation in the regulation of 47 enzymes. Overall, we provided insights and testable predictions covering greater than twice the number of known phosphorylated enzymes in yeast, suggesting extensive phosphorylation-dependent regulation of yeast metabolism.

Protein phosphorylation and its role in archaeal signal transduction

“…2014). Members of almost all arCOG categories were observed to be phosphorylated underpinning its fundamental role.…”

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection

“…Furthermore, metabolomics has proven to be a valuable tool in functional genomics to characterize unknown proteins (Ehebauer et al, 2015). As enzyme inactivation leads to upstream accumulation of metabolites (Fendt et al, 2010), whereas protein activity modulation through post-translational modification or protein interaction also impacts metabolism (Oliveira et al, 2012;Schulz et al, 2014).…”

Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae

“…Lysine metabolism was found to be exclusively enriched ( p -value 0.006) in Lys20 OUT when growing on glucose/proline. While lysine biosynthesis is known to be subject to transcriptional and allosteric control, it was recently shown that Lys20 activity is also regulated by phosphorylation [26, 35]. Metabolite responses in Lys20 OUT were observed only during growth on the poor nitrogen source proline and significant ( p -value < 10 −3 , |log2 fold change| > 0.3785) changes were restricted to the final pathway product lysine and its precursor saccharopine (Fig.…”

“…A notable exception is mass spectrometry-based metabolomics. In particular, it offers the potential to identify small differences in metabolite profiles well before a change of the phenotype is observed [25, 26]. Since many of the phosphoproteins listed in phosphosite databases are part of the metabolic network, metabolomics is a promising approach for probing their functionality.…”