Proteome-wide prediction of acetylation substrates

Amrita Basu, Kristie L. Rose, Junmei Zhang, Ronald C. Beavis, Beatrix Ueberheide, Benjamin A. Garcia, Brian Chait, Yingming Zhao, Donald F. Hunt, Eran Segal, C. David Allis, Sandra B. Hake

Research output: Contribution to journalArticlepeer-review

99 Scopus citations

Abstract

Acetylation is a well-studied posttranslational modification that has been associated with a broad spectrum of biological processes, notably gene regulation. Many studies have contributed to our knowledge of the enzymology underlying acetylation, including efforts to understand the molecular mechanism of substrate recognition by several acetyltransferases, but traditional experiments to determine intrinsic features of substrate site specificity have proven challenging. Here,wecombine experimental methods with clustering analysis of protein sequences to predict protein acetylation based on the sequence characteristics of acetylated lysines within histones with our unique prediction tool PredMod. We define a local amino acid sequence composition that represents potential acetylation sites by implementing a clustering analysis of histone and nonhistone sequences. We show that this sequence composition has predictive power on 2 independent experimental datasets of acetylation marks. Finally, we detect acetylation for selected putative substrates using mass spectrometry, and report several nonhistone acetylated substrates in budding yeast. Our approach, combined with more traditional experimental methods, may be useful for identifying acetylated substrates proteome-wide.

Original languageEnglish
Pages (from-to)13785-13790
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume106
Issue number33
DOIs
StatePublished - Aug 18 2009

Keywords

  • Acetylation
  • Histone
  • Nonhistone
  • PredMod
  • Prediction

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