O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine

O-glycosylation is a protein posttranslational modification important in regulating almost all cells. It is related to a large number of physiological and pathological phenomena. Recognizing O-glycosylation sites is the key to further investigating the molecular mechanism of protein posttranslational modification. This study aimed to collect a reliable dataset on Homo sapiens and develop an O-glycosylation predictor for Homo sapiens, named Captor, through multiple features. A random undersampling method and a synthetic minority oversampling technique were employed to deal with imbalanced data. In addition, the Kruskal–Wallis (K–W) test was adopted to optimize feature vectors and improve the performance of the model. A support vector machine, due to its optimal performance, was used to train and optimize the final prediction model after a comprehensive comparison of various classifiers in traditional machine learning methods and deep learning. On the independent test set, Captor outperformed the existing O-glycosylation tool, suggesting that Captor could provide more instructive guidance for further experimental research on O-glycosylation. The source code and datasets are available at https://github.com/YanZhu06/Captor/ .

Quantitative proteomics analysis of lysine 2-hydroxyisobutyrylation in IgA nephropathy

Background Protein posttranslational modification is an indispensable regulatory element that can fine-tune protein functions and regulate diverse cellular processes. Lysine 2-hydroxyisobutyrylation (Khib) is a protein posttranslational modification that was recently identified and is thought to play a role in a wide variety of active cellular functions. Methods In this report, for the first time, we comparatively studied the 2-hydroxyisobutyrylation proteome in peripheral blood mononuclear cells from a biopsy-proven immunoglobulin A nephropathy (IgAN) group and a normal control group based on liquid chromatography-tandem mass spectrometry. Results Altogether, 7405 proteins were identified and added to a Khib library. Of these proteins, we identified 111 with upregulated expression and 83 with downregulated expression. Furthermore, we identified 428 Khib modification sites on 290 Khib-modified proteins, including 171 sites with increased modification on 122 Khib-modified proteins and 257 specific sites with reduced modification on 168 Khib-modified proteins. Conclusions Importantly, the abundance of lipocalin 2 was increased in the differentially expressed proteins, and a KEGG-based functional enrichment analysis showed that Khib proteins clustered in the IL-17 signaling pathway and phagosome category, which may have important associations with IgAN. Our data enlighten our understanding of Khib in IgAN and indicate that Khib may have important regulatory roles in IgAN.

Quantitative proteomics analysis of lysine 2-hydroxyisobutyrylation in IgA nephropathy

Background: Protein posttranslational modification is an indispensable regulatory element that can fine-tune protein functions and regulate diverse cellular processes. Lysine 2-hydroxyisobutyrylation (Khib) is a protein posttranslational modification that was recently identified and is thought to play a role in a wide variety of active cellular functions. Methods: In this report, for the first time, we comparatively studied the 2-hydroxyisobutyrylation proteome in peripheral blood mononuclear cells from a biopsy-proven immunoglobulin A nephropathy (IgAN) group and a normal control group based on liquid chromatography-tandem mass spectrometry. Results: Altogether, 7405 proteins were identified and added to a Khib library. Of these proteins, we identified 111 with upregulated expression and 83 with downregulated expression. Furthermore, we identified 428 Khib modification sites on 290 Khib-modified proteins, including 171 sites with increased modification on 122 Khib-modified proteins and 257 specific sites with reduced modification on 168 Khib-modified proteins. Conclusions: Importantly, the abundance of lipocalin 2 was increased in the differentially expressed proteins, and a KEGG-based functional enrichment analysis showed that Khib proteins clustered in the IL-17 signaling pathway and phagosome category, which may have important associations with IgAN. Our data enlighten our understanding of Khib in IgAN and indicate that Khib may have important regulatory roles in IgAN.