Stoichiometry of site-specific lysine acetylation in an entire proteome.

TitleStoichiometry of site-specific lysine acetylation in an entire proteome.
Publication TypeJournal Articles
Year of Publication2014
AuthorsBaeza J, Dowell JA, Smallegan MJ, Fan J, Amador-Noguez D, Khan Z, Denu JM
JournalJ Biol Chem
Date Published2014 Aug 1
KeywordsAcetylation, Amino Acid Sequence, Bacterial Proteins, Chromatography, High Pressure Liquid, Computational Biology, Escherichia coli, Lysine, Molecular Sequence Data, Proteome, Tandem Mass Spectrometry

Acetylation of lysine ϵ-amino groups influences many cellular processes and has been mapped to thousands of sites across many organisms. Stoichiometric information of acetylation is essential to accurately interpret biological significance. Here, we developed and employed a novel method for directly quantifying stoichiometry of site-specific acetylation in the entire proteome of Escherichia coli. By coupling isotopic labeling and a novel pairing algorithm, our approach performs an in silico enrichment of acetyl peptides, circumventing the need for immunoenrichment. We investigated the function of the sole NAD(+)-dependent protein deacetylase, CobB, on both site-specific and global acetylation. We quantified 2206 peptides from 899 proteins and observed a wide distribution of acetyl stoichiometry, ranging from less than 1% up to 98%. Bioinformatic analysis revealed that metabolic enzymes, which either utilize or generate acetyl-CoA, and proteins involved in transcriptional and translational processes displayed the highest degree of acetylation. Loss of CobB led to increased global acetylation at low stoichiometry sites and induced site-specific changes at high stoichiometry sites, and biochemical analysis revealed altered acetyl-CoA metabolism. Thus, this study demonstrates that sirtuin deacetylase deficiency leads to both site-specific and global changes in protein acetylation stoichiometry, affecting central metabolism.

Alternate JournalJ. Biol. Chem.
PubMed ID24917678
PubMed Central IDPMC4118097
Grant ListGM065386 / GM / NIGMS NIH HHS / United States
R37 GM059785 / GM / NIGMS NIH HHS / United States
T32 GM007215 / GM / NIGMS NIH HHS / United States