Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels

Background: The addition of an acetyl group to protein N-termini is a widespread co-translational modification. NatB is one of the main N-acetyltransferases that targets a subset of proteins possessing an N-terminal methionine, but so far only a handful of substrates have been reported. Using a yeast nat3 Delta strain, deficient for the catalytic subunit of NatB, we employed a quantitative proteomics strategy to identify NatB substrates and to characterize downstream effects in nat3 Delta. Results: Comparing by proteomics WT and nat3 Delta strains, using metabolic N-15 isotope labeling, we confidently identified 59 NatB substrates, out of a total of 756 detected acetylated protein N-termini. We acquired in-depth proteome wide measurements of expression levels of about 2580 proteins. Most remarkably, NatB deletion led to a very significant change in protein phosphorylation. Conclusions: Protein expression levels change only marginally in between WT and nat3 Delta. A comparison of the detected NatB substrates with their orthologous revealed remarkably little conservation throughout the phylogenetic tree. We further present evidence of post-translational N-acetylation on protein variants at non-annotated N-termini. Moreover, analysis of downstream effects in nat3 Delta revealed elevated protein phosphorylation levels whereby the kinase Snf1p is likely a key element in this process.