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Open Access Research article

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

Andreas O Helbig12, Sara Rosati12, Pim WWM Pijnappel23, Bas van Breukelen125, Marc HTH Timmers23, Shabaz Mohammed12, Monique Slijper12 and Albert JR Heck124*

Author Affiliations

1 Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands

2 Netherlands Proteomics Centre, Padualaan 8, Utrecht, 3584 CH, The Netherlands

3 University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands

4 Center for Biomedical Genetics, MCU, Stratenum 3.223, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands

5 Netherlands Bioinformatics Centre, Geert Grooteplein 28, Nijmgen, 6525 GA, The Netherlands

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BMC Genomics 2010, 11:685  doi:10.1186/1471-2164-11-685

Published: 2 December 2010

Abstract

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 nat3Δ strain, deficient for the catalytic subunit of NatB, we employed a quantitative proteomics strategy to identify NatB substrates and to characterize downstream effects in nat3Δ.

Results

Comparing by proteomics WT and nat3Δ strains, using metabolic 15N 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 nat3Δ. 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 nat3Δ revealed elevated protein phosphorylation levels whereby the kinase Snf1p is likely a key element in this process.