Proteome-wide prediction of acetylation substrates.
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, we combine 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.
Basu
Amrita
A
Laboratory of Chromatin Biology, Rockefeller University, New York, NY 10065, USA.
Rose
Kristie L
KL
Zhang
Junmei
J
Beavis
Ronald C
RC
Ueberheide
Beatrix
B
Garcia
Benjamin A
BA
Chait
Brian
B
Zhao
Yingming
Y
Hunt
Donald F
DF
Segal
Eran
E
Allis
C David
CD
Hake
Sandra B
SB
D000107:Acetylation; D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D006657:Histones / Q000737:chemistry; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D012372:ROC Curve; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000502:physiology
D006657:Histones; D011506:Proteins; D020543:Proteome