GPS-SUMO: a Tool for the Prediction of Sumoylation Sites and SUMO-interaction Motifs

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2014 Jun 2

PMID 24880689

Citations 254

Authors

Qi Zhao

Yubin Xie

Yueyuan Zheng

Shuai Jiang

Wenzhong Liu

Weiping Mu

Zexian Liu

Yong Zhao

Yu Xue

Jian Ren

Affiliations

Soon will be listed here.

Abstract

Small ubiquitin-like modifiers (SUMOs) regulate a variety of cellular processes through two distinct mechanisms, including covalent sumoylation and non-covalent SUMO interaction. The complexity of SUMO regulations has greatly hampered the large-scale identification of SUMO substrates or interaction partners on a proteome-wide level. In this work, we developed a new tool called GPS-SUMO for the prediction of both sumoylation sites and SUMO-interaction motifs (SIMs) in proteins. To obtain an accurate performance, a new generation group-based prediction system (GPS) algorithm integrated with Particle Swarm Optimization approach was applied. By critical evaluation and comparison, GPS-SUMO was demonstrated to be substantially superior against other existing tools and methods. With the help of GPS-SUMO, it is now possible to further investigate the relationship between sumoylation and SUMO interaction processes. A web service of GPS-SUMO was implemented in PHP+JavaScript and freely available at http://sumosp.biocuckoo.org.

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References

Li W, Godzik A . Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006; 22(13):1658-9. DOI: 10.1093/bioinformatics/btl158. View

Zhu J, Zhu S, Guzzo C, Ellis N, Sung K, Choi C . Small ubiquitin-related modifier (SUMO) binding determines substrate recognition and paralog-selective SUMO modification. J Biol Chem. 2008; 283(43):29405-15. PMC: 2570875. DOI: 10.1074/jbc.M803632200. View

Xu J, He Y, Qiang B, Yuan J, Peng X, Pan X . A novel method for high accuracy sumoylation site prediction from protein sequences. BMC Bioinformatics. 2008; 9:8. PMC: 2245905. DOI: 10.1186/1471-2105-9-8. View

Rodriguez M, Dargemont C, Hay R . SUMO-1 conjugation in vivo requires both a consensus modification motif and nuclear targeting. J Biol Chem. 2001; 276(16):12654-9. DOI: 10.1074/jbc.M009476200. View

Stark C, Su T, Breitkreutz A, Lourenco P, Dahabieh M, Breitkreutz B . PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. Database (Oxford). 2010; 2010:bap026. PMC: 2860897. DOI: 10.1093/database/bap026. View

Song J, Durrin L, Wilkinson T, Krontiris T, Chen Y . Identification of a SUMO-binding motif that recognizes SUMO-modified proteins. Proc Natl Acad Sci U S A. 2004; 101(40):14373-8. PMC: 521952. DOI: 10.1073/pnas.0403498101. View

Hornbeck P, Kornhauser J, Tkachev S, Zhang B, Skrzypek E, Murray B . PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 2011; 40(Database issue):D261-70. PMC: 3245126. DOI: 10.1093/nar/gkr1122. View

Kerscher O, Felberbaum R, Hochstrasser M . Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu Rev Cell Dev Biol. 2006; 22:159-80. DOI: 10.1146/annurev.cellbio.22.010605.093503. View

Xue Y, Liu Z, Gao X, Jin C, Wen L, Yao X . GPS-SNO: computational prediction of protein S-nitrosylation sites with a modified GPS algorithm. PLoS One. 2010; 5(6):e11290. PMC: 2892008. DOI: 10.1371/journal.pone.0011290. View

10.

Hannich J, Lewis A, Kroetz M, Li S, Heide H, Emili A . Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J Biol Chem. 2004; 280(6):4102-10. DOI: 10.1074/jbc.M413209200. View

11.

Lee L, Sakurai M, Matsuzaki S, Arancio O, Fraser P . SUMO and Alzheimer's disease. Neuromolecular Med. 2013; 15(4):720-36. PMC: 3823823. DOI: 10.1007/s12017-013-8257-7. View

12.

Gill G . Something about SUMO inhibits transcription. Curr Opin Genet Dev. 2005; 15(5):536-41. DOI: 10.1016/j.gde.2005.07.004. View

13.

Melchior F . SUMO--nonclassical ubiquitin. Annu Rev Cell Dev Biol. 2000; 16:591-626. DOI: 10.1146/annurev.cellbio.16.1.591. View

14.

Zhao J . Sumoylation regulates diverse biological processes. Cell Mol Life Sci. 2007; 64(23):3017-33. PMC: 7079795. DOI: 10.1007/s00018-007-7137-4. View

15.

Ren J, Gao X, Jin C, Zhu M, Wang X, Shaw A . Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0. Proteomics. 2018; 9(12):3409-3412. DOI: 10.1002/pmic.200800646. View

16.

Chen Y, Chen Z, Gong Y, Ying G . SUMOhydro: a novel method for the prediction of sumoylation sites based on hydrophobic properties. PLoS One. 2012; 7(6):e39195. PMC: 3375222. DOI: 10.1371/journal.pone.0039195. View

17.

Geiss-Friedlander R, Melchior F . Concepts in sumoylation: a decade on. Nat Rev Mol Cell Biol. 2007; 8(12):947-56. DOI: 10.1038/nrm2293. View

18.

Xue Y, Zhou F, Fu C, Xu Y, Yao X . SUMOsp: a web server for sumoylation site prediction. Nucleic Acids Res. 2006; 34(Web Server issue):W254-7. PMC: 1538802. DOI: 10.1093/nar/gkl207. View

19.

Sampson D, Wang M, Matunis M . The small ubiquitin-like modifier-1 (SUMO-1) consensus sequence mediates Ubc9 binding and is essential for SUMO-1 modification. J Biol Chem. 2001; 276(24):21664-9. DOI: 10.1074/jbc.M100006200. View

20.

Dinkel H, Chica C, Via A, Gould C, Jensen L, Gibson T . Phospho.ELM: a database of phosphorylation sites--update 2011. Nucleic Acids Res. 2010; 39(Database issue):D261-7. PMC: 3013696. DOI: 10.1093/nar/gkq1104. View