YPIBP: A repository for phosphoinositide-binding proteins in yeast

Jagat Rathod; Han-Chen Yen; Biqing Liang; Yan-Yuan Tseng; Chien-Sheng Chen; Wei-Sheng Wu

doi:10.1016/j.csbj.2021.06.035

YPIBP: A repository for phosphoinositide-binding proteins in yeast

Comput Struct Biotechnol J. 2021 Jun 24:19:3692-3707. doi: 10.1016/j.csbj.2021.06.035. eCollection 2021.

Authors

Jagat Rathod¹, Han-Chen Yen², Biqing Liang¹, Yan-Yuan Tseng³, Chien-Sheng Chen^{4

5}, Wei-Sheng Wu²

Affiliations

¹ Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan.
² Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan.
³ Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, MI 48201, USA.
⁴ Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan.
⁵ Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan.

Abstract

Phosphoinositides (PIs) are a family of eight lipids consisting of phosphatidylinositol (PtdIns) and its seven phosphorylated forms. PIs have important regulatory functions in the cell including lipid signaling, protein transport, and membrane trafficking. Yeast has been recognized as a eukaryotic model system to study lipid-protein interactions. Hundreds of yeast PI-binding proteins have been identified, but this research knowledge remains scattered. Besides, the complete PI-binding spectrum and potential PI-binding domains have not been interlinked. No comprehensive databases are available to support the lipid-protein interaction research on phosphoinositides. Here we constructed the first knowledgebase of Yeast Phosphoinositide-Binding Proteins (YPIBP), a repository consisting of 679 PI-binding proteins collected from high-throughput proteome-array and lipid-array studies, QuickGO, and a rigorous literature mining. The YPIBP also contains protein domain information in categories of lipid-binding domains, lipid-related domains and other domains. The YPIBP provides search and browse modes along with two enrichment analyses (PI-binding enrichment analysis and domain enrichment analysis). An interactive visualization is given to summarize the PI-domain-protein interactome. Finally, three case studies were given to demonstrate the utility of YPIBP. The YPIBP knowledgebase consolidates the present knowledge and provides new insights of the PI-binding proteins by bringing comprehensive and in-depth interaction network of the PI-binding proteins. YPIBP is available at http://cosbi7.ee.ncku.edu.tw/YPIBP/.

Keywords: ANTH, AP180 N-terminal Homology; BAR, Bin-Amphiphysin-Rvs; CAFA, Critical Assessment of Functional Annotation; CRAL-TRIO, cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor; Cvt, Cytoplasm-to-vacuole targeting; ENTH, Epsin N-terminal Homology; FDR, False Discovery Rate; FYVE, Fab 1 (yeast orthologue of PIKfyve), YOTB, Vac 1 (vesicle transport protein), and EEA1; GO, Gene Ontology; ITC, Isothermal Titration Calorimetry; LBD, Lipid-Binding Domain; LMPD, LIPID MAPS Proteome Database; LMSD, LIPID MAPS Structure Database; LRD, Lipid-Related Domain; Lipid-binding domain; OMIM, Online Mendelian Inheritance in Man; OSBP, Oxysterol-Binding Protein; PH, Pleckstrin Homology; PI(3,4)P2, phosphatidylinositol-3,4-bisphosphate; PI(3,4,5)P3, phosphatidylinositol-3,4,5-trisphosphate; PI(3,5)P2, phosphatidylinositol-3,5-bisphosphate; PI(4,5)P2, phosphatidylinositol-4,5-bisphosphate; PI-binding protein; PI3P, phosphatidylinositol-3-phosphate; PI4P, phosphatidylinositol-4-phosphate; PI5P, phosphatidylinositol-5-phosphate; PIs, Phosphoinositides; PMID, PubMed ID; PX, Phox Homology; Phosphatidylinositol (PtdIns); Phosphoinositides (PIs); PtdIns, Phosphatidylinositol; QCM, Quartz Crystal Microbalance; S. cerevisiae; SNX, Sorting Nexin; SPR, Surface Plasmon Resonance; YPIBP, Yeast Phosphoinositide-Binding Proteins; Yeast.