N-terminal Acetylation Levels Are Maintained During Acetyl-CoA Deficiency in Saccharomyces cerevisiae

• Published in: Molecular & cellular proteomics Vol. 17; no. 12; pp. 2309 - 2323
• Main Authors: Varland, Sylvia, Aksnes, Henriette, Kryuchkov, Fedor, Impens, Francis, Van Haver, Delphi, Jonckheere, Veronique, Ziegler, Mathias, Gevaert, Kris, Van Damme, Petra, Arnesen, Thomas
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2018; The American Society for Biochemistry and Molecular Biology
• Subjects: Acetyl coenzyme A; Acetyl Coenzyme A - metabolism; Acetylation; Acetyltransferases - metabolism; Analysis of Variance; Cells, Cultured; Chi-Square Distribution; Cyclins - metabolism; Histones - metabolism; Metabolism; Molecular biology; N-terminal acetylation; N-Terminal Acetyltransferases - metabolism; N-terminal modifications; N-terminomics; Proteome - metabolism; Ribosomal proteins; Ribosomal Proteins - metabolism; Saccharomyces cerevisiae - enzymology; Saccharomyces cerevisiae Proteins - metabolism; Tandem Mass Spectrometry; Yeast; Tandem Mass Spectrometry; Yeast; Ribosomal proteins; N-terminal acetylation; N-terminomics; N-terminal modifications; Acetyl coenzyme A; Acetylation; Molecular biology; Metabolism
• ISSN: 1535-9476; 1535-9484; 1535-9484
• DOI: 10.1074/mcp.RA118.000982

Nt-acetylation is a prevalent protein modification catalyzed by N-terminal acetyltransferases using acetyl-CoA as acetyl donor. Here, we performed a global analysis of Nt-acetylation in yeast following nutrient starvation. Contrary to histone acetylation, which is sensitive to acetyl-CoA levels, we demonstrate that Nt-acetylation remains largely unaffected to changes in cellular metabolism. We did, however, identify two protein groups that were differentially Nt-acetylated, one showing the same sensitivity to acetyl-CoA as histones. We propose that specific, rather than global, Nt-acetylation events are subject to metabolic regulation. [Display omitted] Highlights •First global study on metabolic regulation of Nt-acetylation.•Yeast cells maintain global Nt-acetylation levels during prolonged starvation.•Nt-acetylation can in some cases be either up- or downregulated by starvation.•Naa10/NatA affects the steady-state protein levels of Rsa3 and Rpl7a. N-terminal acetylation (Nt-acetylation) is a highly abundant protein modification in eukaryotes and impacts a wide range of cellular processes, including protein quality control and stress tolerance. Despite its prevalence, the mechanisms regulating Nt-acetylation are still nebulous. Here, we present the first global study of Nt-acetylation in yeast cells as they progress to stationary phase in response to nutrient starvation. Surprisingly, we found that yeast cells maintain their global Nt-acetylation levels upon nutrient depletion, despite a marked decrease in acetyl-CoA levels. We further observed two distinct sets of protein N termini that display differential and opposing Nt-acetylation behavior upon nutrient starvation, indicating a dynamic process. The first protein cluster was enriched for annotated N termini showing increased Nt-acetylation in stationary phase compared with exponential growth phase. The second protein cluster was conversely enriched for alternative nonannotated N termini (i.e. N termini indicative of shorter N-terminal proteoforms) and, like histones, showed reduced acetylation levels in stationary phase when acetyl-CoA levels were low. Notably, the degree of Nt-acetylation of Pcl8, a negative regulator of glycogen biosynthesis and two components of the pre-ribosome complex (Rsa3 and Rpl7a) increased during starvation. Moreover, the steady-state levels of these proteins were regulated both by starvation and NatA activity. In summary, this study represents the first comprehensive analysis of metabolic regulation of Nt-acetylation and reveals that specific, rather than global, Nt-acetylation events are subject to metabolic regulation.