title: Validation of the reliability of computational O-GlcNAc prediction.
abstract: O-GlcNAcylation is an inducible, highly dynamic and reversible posttranslational modification, which regulates numerous cellular processes such as gene expression, translation, immune reactions, protein degradation, protein-protein interaction, apoptosis, and signal transduction. In contrast to N-linked glycosylation, O-GlcNAcylation does not display a strict amino acid consensus sequence, although serine or threonine residues flanked by proline and valine are preferred sites of O-GlcNAcylation. Based on this information, computational prediction tools of O-GlcNAc sites have been developed. Here, we retrospectively assessed the performance of two available O-GlcNAc prediction programs YinOYang 1.2 server and OGlcNAcScan by comparing their predictions for recently discovered experimentally validated O-GlcNAc sites. Both prediction programs efficiently identified O-GlcNAc sites situated in an environment resembling the consensus sequence P-P-V-[ST]-T-A. However, both prediction programs revealed numerous false negative O-GlcNAc predictions when the site of modification was located in an amino acid sequence differing from the known consensus sequence. By searching for a common sequence motif, we found that O-GlcNAcylation of nucleocytoplasmic proteins preferably occurs at serine and threonine residues flanked downstream by proline and valine and upstream by one to two alanines followed by a stretch of serine and threonine residues. However, O-GlcNAcylation of proteins located in the mitochondria or in the secretory lumen occurs at different sites and does not follow a distinct consensus sequence. Thus, our study indicates the limitations of the presently available computational prediction methods for O-GlcNAc sites and suggests that experimental validation is mandatory. Continuously update and further development of available databases will be the key to improve the performance of O-GlcNAc site prediction.
authors: Division of Molecular and Experimental Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Schwabachanlage 10, 91054 Erlangen, Germany. Electronic address: r.jochmann@gmx.de.
authors: Ramona
authors: R
authors: Jochmann
authors: Division of Molecular and Experimental Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Schwabachanlage 10, 91054 Erlangen, Germany. Electronic address: patrick.holz@uk-erlangen.de.
authors: Patrick
authors: P
authors: Holz
authors: Institute of Biochemistry, University of Erlangen-Nuremberg, Fahrstr. 17, 91054 Erlangen, Germany. Electronic address: heinrich.sticht@fau.de.
authors: Heinrich
authors: H
authors: Sticht
authors: Division of Molecular and Experimental Surgery, University Medical Center Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Schwabachanlage 10, 91054 Erlangen, Germany. Electronic address: michael.stuerzl@uk-erlangen.de.
authors: Michael
authors: M
authors: Stürzl
mesh_terms: D000117:Acetylglucosamine / Q000378:metabolism*; D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D016384:Consensus Sequence; D005544:Forecasting; D006801:Humans; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012189:Retrospective Studies; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins; D000117:Acetylglucosamine
keywords: O-GlcNAc; OGlcNAcScan; Prediction program; YinOYang server; dbOGAP database