دورية أكاديمية
YPIBP: A repository for phosphoinositide-binding proteins in yeast.
| العنوان: | YPIBP: A repository for phosphoinositide-binding proteins in yeast. |
|---|---|
| المؤلفون: | Rathod J; Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan., Yen HC; Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan., Liang B; Department of Earth Sciences, College of Sciences, National Cheng Kung University, Tainan 701, Taiwan., Tseng YY; Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, MI 48201, USA., Chen CS; Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan.; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan., Wu WS; Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan. |
| المصدر: | Computational and structural biotechnology journal [Comput Struct Biotechnol J] 2021 Jun 24; Vol. 19, pp. 3692-3707. Date of Electronic Publication: 2021 Jun 24 (Print Publication: 2021). |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology Country of Publication: Netherlands NLM ID: 101585369 Publication Model: eCollection Cited Medium: Print ISSN: 2001-0370 (Print) Linking ISSN: 20010370 NLM ISO Abbreviation: Comput Struct Biotechnol J Subsets: PubMed not MEDLINE |
| أسماء مطبوعة: | Publication: Amsterdam : Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology Original Publication: Gothenburg, Sweden : Research Network of Computational and Structural Biotechnology |
| مستخلص: | 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/. Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. (© 2021 The Author(s).) |
| References: | PLoS One. 2013 May 07;8(5):e61951. (PMID: 23667450) Mol Biol Cell. 1998 Aug;9(8):1981-94. (PMID: 9693361) EMBO J. 2016 Mar 15;35(6):561-79. (PMID: 26888746) PLoS One. 2018 Jul 26;13(7):e0201204. (PMID: 30048518) Integr Biol (Camb). 2012 Mar;4(3):247-58. (PMID: 22327461) FEBS Lett. 2007 May 22;581(11):2105-11. (PMID: 17316616) FEBS Lett. 2002 Feb 20;513(1):11-8. (PMID: 11911874) Chem Phys Lipids. 2014 Sep;182:3-18. (PMID: 24556335) Biochem J. 2000 Oct 1;351(Pt 1):19-31. (PMID: 11001876) Protein Sci. 1999 Feb;8(2):435-8. (PMID: 10048338) Sci STKE. 2003 Dec 16;2003(213):re16. (PMID: 14679290) Nucleic Acids Res. 2006 Jan 1;34(Database issue):D507-10. (PMID: 16381922) Biochim Biophys Acta Mol Cell Biol Lipids. 2019 Mar;1864(3):433-442. (PMID: 30670192) Cell Rep. 2015 Sep 1;12(9):1519-30. (PMID: 26299969) Adv Exp Med Biol. 2019;1111:1-17. (PMID: 29569114) Nature. 1998 Jul 30;394(6692):433-4. (PMID: 9697765) Lipid Insights. 2015 Nov 12;8(Suppl 1):1-9. (PMID: 26715851) Mol Biol Cell. 2005 Feb;16(2):717-30. (PMID: 15574875) Anal Chem. 2021 Jan 19;93(2):868-877. (PMID: 33302626) BMC Syst Biol. 2015 Dec 29;9:96. (PMID: 26714768) Mol Cell Proteomics. 2012 Nov;11(11):1177-90. (PMID: 22843995) FEBS Lett. 2010 Apr 2;584(7):1359-66. (PMID: 20146925) Dev Cell. 2003 Sep;5(3):499-511. (PMID: 12967568) Mol Biol Cell. 2018 Sep 1;29(18):2190-2200. (PMID: 29949447) Science. 1996 Mar 15;271(5255):1533-9. (PMID: 8599109) Genetics. 2011 Nov;189(3):695-704. (PMID: 22084421) Biomed Rep. 2017 Aug;7(2):153-158. (PMID: 28804628) FEBS Lett. 2001 Oct 12;506(3):173-9. (PMID: 11602240) BMC Bioinformatics. 2008 Dec 05;9:522. (PMID: 19061501) J Biol Chem. 2002 Aug 16;277(33):30198-207. (PMID: 12048214) Trends Cell Biol. 2013 Jan;23(1):1-8. (PMID: 22980035) Nat Methods. 2014 Jan;11(1):47-50. (PMID: 24270602) Anal Biochem. 2011 Mar 1;410(1):77-83. (PMID: 21094116) Nucleic Acids Res. 2012 Jan;40(Database issue):D700-5. (PMID: 22110037) J Physiol. 2010 Sep 1;588(Pt 17):3179-85. (PMID: 20519312) Sci Adv. 2020 Feb 19;6(8):eaay5736. (PMID: 32128410) J Bacteriol. 1991 Mar;173(6):2026-34. (PMID: 2002005) Biol Pharm Bull. 2007 Sep;30(9):1599-604. (PMID: 17827706) Plant Physiol. 2004 Oct;136(2):3080-94; discussion 3001-2. (PMID: 15466235) Physiol Rev. 2013 Jul;93(3):1019-137. (PMID: 23899561) Nucleic Acids Res. 2018 Jan 4;46(D1):D736-D742. (PMID: 29140510) Prog Lipid Res. 2016 Jan;61:30-9. (PMID: 26658141) Integr Biol (Camb). 2015 Aug;7(8):846-58. (PMID: 26079294) Chem Rev. 2019 May 8;119(9):5775-5848. (PMID: 30758191) J Lipid Res. 2009 Apr;50 Suppl:S299-304. (PMID: 19008549) Mol Syst Biol. 2010 Nov 30;6:430. (PMID: 21119626) Curr Opin Cell Biol. 2018 Aug;53:52-60. (PMID: 29859321) Nucleic Acids Res. 2019 Jan 8;47(D1):D529-D541. (PMID: 30476227) Bioinformatics. 2009 Nov 15;25(22):3045-6. (PMID: 19744993) Prog Lipid Res. 2007 Nov;46(6):315-27. (PMID: 17707914) Proc Natl Acad Sci U S A. 2017 Nov 21;114(47):E10112-E10121. (PMID: 29114050) J Biochem. 2020 Oct 1;168(4):329-336. (PMID: 32745205) J Am Soc Mass Spectrom. 2017 Apr;28(4):579-586. (PMID: 27924494) Anal Biochem. 2017 Jan 1;516:9-12. (PMID: 27742211) J Biol Chem. 2004 Feb 6;279(6):4175-9. (PMID: 14630930) Cold Spring Harb Perspect Biol. 2011 Aug 01;3(8):a004796. (PMID: 21576256) Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11829-34. (PMID: 20547830) Nature. 1998 Jul 30;394(6692):432-3. (PMID: 9697764) Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2281-90. (PMID: 24843134) PLoS One. 2014 Sep 25;9(9):e108368. (PMID: 25255026) Biochemistry. 2001 Jul 24;40(29):8581-7. (PMID: 11456498) Science. 2001 Sep 14;293(5537):2101-5. (PMID: 11474067) Nucleic Acids Res. 2007 Jan;35(Database issue):D527-32. (PMID: 17098933) J Biol Chem. 2000 Jun 9;275(23):17878-85. (PMID: 10747966) Nat Rev Mol Cell Biol. 2015 Dec;16(12):753-61. (PMID: 26507169) BMC Bioinformatics. 2017 Jul 10;18(1):331. (PMID: 28693421) Bioinformatics. 2015 Sep 1;31(17):2860-6. (PMID: 25943471) Curr Opin Chem Biol. 2014 Aug;21:144-53. (PMID: 25129056) J Cell Sci. 2004 Jan 1;117(Pt 1):9-18. (PMID: 14657269) Sci STKE. 2002 Apr 23;2002(129):pl6. (PMID: 11972359) Biochim Biophys Acta. 2012 Feb;1818(2):172-7. (PMID: 21763269) Mol Cell. 1998 Jul;2(1):157-62. (PMID: 9702203) |
| معلومات مُعتمدة: | R01 CA204962 United States CA NCI NIH HHS |
| فهرسة مساهمة: | 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 |
| تواريخ الأحداث: | Date Created: 20210721 Latest Revision: 20240505 |
| رمز التحديث: | 20240505 |
| مُعرف محوري في PubMed: | PMC8261538 |
| DOI: | 10.1016/j.csbj.2021.06.035 |
| PMID: | 34285772 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 2001-0370 |
|---|---|
| DOI: | 10.1016/j.csbj.2021.06.035 |