Abstract
Prokaryotic proteins are regulated by pupylation, a type of post-translational modification that contributes to cellular function in bacterial organisms. In pupylation process, the prokaryotic ubiquitin-like protein (Pup) tagging is functionally analogous to ubiquitination in order to tag target proteins for proteasomal degradation. To date, several experimental methods have been developed to identify pupylated proteins and their pupylation sites, but these experimental methods are generally laborious and costly. Therefore, computational methods that can accurately predict potential pupylation sites based on protein sequence information are highly desirable. In this paper, a novel predictor termed as pbPUP has been developed for accurate prediction of pupylation sites. In particular, a sophisticated sequence encoding scheme [i.e. the profile-based composition of k-spaced amino acid pairs (pbCKSAAP)] is used to represent the sequence patterns and evolutionary information of the sequence fragments surrounding pupylation sites. Then, a Support Vector Machine (SVM) classifier is trained using the pbCKSAAP encoding scheme. The final pbPUP predictor achieves an AUC value of 0.849 in10-fold cross-validation tests and outperforms other existing predictors on a comprehensive independent test dataset. The proposed method is anticipated to be a helpful computational resource for the prediction of pupylation sites. The web server and curated datasets in this study are freely available at http://protein.cau.edu.cn/pbPUP/.
Highlights
The bacterial prokaryotic ubiquitin-like protein (Pup) is initially perceived as a small protein related to post-translational modifications (PTMs)
The window size is an important factor of the prediction performance, which reflects the influence of surrounding residues on the discrimination of pupylation from non-pupylation sites
The Support Vector Machine (SVM) parameters were optimized through the grid search, and the corresponding areas under the ROC curves (AUCs) value was obtained from the 10-fold cross-validation test on the training set
Summary
The bacterial prokaryotic ubiquitin-like protein (Pup) is initially perceived as a small protein related to post-translational modifications (PTMs). Pup is an intrinsically unstructured protein consisting of 64 amino acids [1, 2]. The ubiquitin-proteasome degradation pathway was discovered in the late 1970's [6], while the analogous Pup-proteasome pathway was not identified in prokaryotes until recently [5, 7, 8]. The proteasomal Pup has been discovered in the phyla Actinobacteria and Nitrospira species [9]. The evidence of Pup proteasome degradation pathway has been rapidly accumulating in both the in vitro [10, 11] and in vivo systems [12]
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