Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation

• Published in: PloS one 2011-12, Vol.6 (12), p.e28228-e28228
• Main Authors: Lu, Zhike, Cheng, Zhongyi, Zhao, Yingming, Volchenboum, Samuel L
• Format: Article
• Language: English
• Subjects: Acetates; Acetylation; Analysis; Animals; Bioinformatics; Biology; Cancer; Cell Cycle; Cellular structure; Chromatin; Compartments; Computational Biology - methods; Crosstalk; Deoxyribonucleic acid; Diabetes; DNA; DNA damage; DNA methylation; DNA Repair; DNA structure; Drosophila; Encyclopedias; Gene Expression Regulation; Genes; Genomes; Heat shock proteins; Helices; Humans; Insects; Kinases; Localization; Lysine; Lysine - chemistry; Medical research; Methylation; Mice; Models, Biological; Phosphorylation; Post-translation; Post-translational modifications; Predictions; Protein Conformation; Protein Processing, Post-Translational; Protein structure; Protein Structure, Secondary; Protein Structure, Tertiary; Proteins; Proteomics; Proteomics - methods; Regulation; Secondary structure; Signal transduction; Studies; Translation; Ubiquitin; Ubiquitin - chemistry; Ubiquitination
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0028228

Recent proteomics studies suggest high abundance and a much wider role for lysine acetylation (K-Ac) in cellular functions. Nevertheless, cross influence between K-Ac and other post-translational modifications (PTMs) has not been carefully examined. Here, we used a variety of bioinformatics tools to analyze several available K-Ac datasets. Using gene ontology databases, we demonstrate that K-Ac sites are found in all cellular compartments. KEGG analysis indicates that the K-Ac sites are found on proteins responsible for a diverse and wide array of vital cellular functions. Domain structure prediction shows that K-Ac sites are found throughout a wide variety of protein domains, including those in heat shock proteins and those involved in cell cycle functions and DNA repair. Secondary structure prediction proves that K-Ac sites are preferentially found in ordered structures such as alpha helices and beta sheets. Finally, by mutating K-Ac sites in silico and predicting the effect on nearby phosphorylation sites, we demonstrate that the majority of lysine acetylation sites have the potential to impact protein phosphorylation, methylation, and ubiquitination status. Our work validates earlier smaller-scale studies on the acetylome and demonstrates the importance of PTM crosstalk for regulation of cellular function.