JASSA: A comprehensive tool for prediction of SUMOylation sites and SIMs

Bioinformatics

Volumn 31, Issue 21, 2015, Pages 3483-3491

  Beauclair, Guillaume ^a,b,c,e   Bridier Nahmias, Antoine ^a,b,c,d   Zagury, Jean François ^d   Säb, Ali ^a,b,c,d   Zamborlini, Alessia ^a,b,c,d  

^a SAINT LOUIS HOSPITAL   (France)

^b Institut Universitaire d'Hématologie   (France)

^c UNIVERSITÉ PARIS DESCARTES   (France)

^d University of Paris Cité   (France)

^e HANNOVER MEDICAL SCHOOL   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

SUMO PROTEIN;

COMPUTER PROGRAM; HUMAN; METABOLISM; PROCEDURES; PROTEIN DOMAIN; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SUMOYLATION;

HUMANS; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SMALL UBIQUITIN-RELATED MODIFIER PROTEINS; SOFTWARE; SUMOYLATION;

EID: 84947557944     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv403     Document Type: Article

References (45)

1. Apweiler,R. et al. (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res., 32, D115-D119.
2. Benson,M.D. et al. (2007) SUMO modification regulates inactivation of the voltage-gated potassium channel Kv1.5. Proc. Natl. Acad. Sci. U. S. A., 104, 1805-1810.
3. Blomster,H.A. et al. (2009) Novel proteomics strategy brings insight into the prevalence of SUMO-2 target sites. Mol. Cell. Proteomics, 8, 1382-1390.
4. Chang,C.-C. et al. (2011) Structural and functional roles of Daxx SIM phosphorylation in SUMO paralog-selective binding and apoptosis modulation. Mol. Cell, 42, 62-74.
5. Chen,Y.-Z. et al. (2012) SUMOhydro: a novel method for the prediction of sumoylation sites based on hydrophobic properties. PLoS One, 7, e39195.
6. Crooks,G.E. et al. (2004) WebLogo: a sequence logo generator. Genome Res., 14, 1188-1190.
7. Droescher,M. et al. (2013) SUMO rules: regulatory concepts and their implication in neurologic functions. Neuromolecular Med., 15, 639-660.
8. Flotho,A. and Melchior,F. (2013) Sumoylation: a regulatory protein modification in health and disease. Annu. Rev. Biochem., 82, 357-385.
9. Gareau,J.R. and Lima,C.D. (2011) The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nat. Rev. Mol. Cell Biol., 11, 861-871.
10. Hannich, J.T. et al. (2005) Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J. Biol. Chem., 280, 4102-4110.
11. Hecker,C.-M. et al. (2006) Specification of SUMO1- and SUMO2-interacting motifs. J. Biol. Chem., 281, 16117-16127.
12. Hendriks,I.A. et al. (2014) Uncovering global SUMOylation signaling networks in a site-specific manner. Nat Struct. Mol. Biol., 21, 927-936.
13. Hietakangas,V. et al. (2006) PDSM, a motif for phosphorylation-dependent SUMO modification. Proc. Natl. Acad. Sci. U. S. A., 103, 45-50.
14. Hornbeck,P.V. et al. (2004) PhosphoSite: a bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics, 4, 1551-1561.
15. Impens,F. et al. (2014) Mapping of SUMO sites and analysis of SUMOylation changes induced by external stimuli. Proc. Natl Acad. Sci. U.S.A., 111, 12432-12437.
16. Ivanov,A.V. et al. (2007) PHD domain-mediated E3 ligase activity directs intramolecular sumoylation of an adjacent bromodomain required for gene silencing. Mol. Cell, 28, 823-837.
17. Kerscher,O. (2007) SUMO junction-what's your function? New insights through SUMO-interacting motifs. EMBO Rep., 8, 550-555.
18. Matic,I. et al. (2010) Site-specific identification of SUMO-2 targets in cells reveals an inverted SUMOylation motif and a hydrophobic cluster SUMOylation motif. Mol. Cell, 39, 1-19.
19. Melchior,F. (2000) SUMO - nonclassical ubiquitin. Annu. Rev. Cell Dev. Biol., 16, 591-626.
20. Meulmeester,E. et al. (2008) Mechanism and consequences for paralog-specific sumoylation of ubiquitin-specific protease 25. Mol. Cell, 30, 610-619.
21. Minty,A. et al. (2000) Covalent modification of p73alpha by SUMO-1. Two-hybrid screening with p73 identifies novel SUMO-1-interacting proteins and a SUMO-1 interaction motif. J. Biol. Chem., 275, 36316-36323.
22. Miteva,M. et al. (2010) Sumoylation as a signal for polyubiquitylation and proteasomal degradation. Subcell. Biochem., 54, 195-214.
23. Mohideen,F. et al. (2009) A molecular basis for phosphorylation-dependent SUMO conjugation by the E2 UBC9. Nat. Struct. Mol. Biol., 16, 945-952.
24. Ouyang,J. et al. (2009) Direct binding of CoREST1 to SUMO-2/3 contributes to gene-specific repression by the LSD1/CoREST1/HDAC complex. Mol. Cell, 34, 145-154.
25. Picard,N. et al. (2012) Identification of estrogen receptor β as a SUMO-1 target reveals a novel phosphorylated sumoylation motif and regulation by glycogen synthase kinase 3b. Mol. Cell. Biol., 32, 2709-2721.
26. Pichler,A. et al. (2005) SUMO modification of the ubiquitin-conjugating enzyme E2-25K. Nat. Struct. Mol. Biol., 12, 264-269.
27. R Core Team (2015) R: a Language and Environment for Statistical Computing. R Foundation for Statistical Computing Vienna, Austria.
28. Ren,J. et al. (2009) Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0. Proteomics, 9, 3409-3412.
29. Robin,X. et al. (2011) pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics, 12, 77.
30. Rodriguez,M.S. et al. (2001) SUMO-1 conjugation in vivo requires both a consensus modification motif and nuclear targeting. J. Biol. Chem., 276, 12654-12659.
31. Stankovic-Valentin,N. et al. (2007) An acetylation/deacetylation-SUMOylation switch through a phylogenetically conserved psiKXEP motif in the tumor suppressor HIC1 regulates transcriptional repression activity. Mol. Cell. Biol., 27, 2661-2675.
32. Sampson,D.A. et al. (2001) The small ubiquitin-like modifier-1 (SUMO-1) consensus sequence mediates Ubc9 binding and is essential for SUMO-1 modification. J. Biol. Chem., 276, 21664-21669.
33. Sarge,K.D. and Park-Sarge,O.-K. (2009) Sumoylation and human disease pathogenesis. Trends Biochem. Sci., 34, 200-205.
34. Sekiyama,N. et al. (2008) Structure of the small ubiquitin-like modifier (SUMO)-interacting motif of MBD1-containing chromatin-associated factor 1 bound to SUMO-3. J. Biol. Chem., 283, 35966-35975.
35. Song,J. et al. (2005) Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation. J. Biol. Chem., 280, 40122-40129.
36. Subramanian,L. et al. (2003) A synergy control motif within the attenuator domain of CCAAT/enhancer-binding protein alpha inhibits transcriptional synergy through its PIASy-enhanced modification by SUMO-1 or SUMO-3. J. Biol. Chem., 278, 9134-9141.
37. Sun,H. and Hunter,T. (2012) Poly-small ubiquitin-like modifier (PolySUMO)-binding proteins identified through a string search. J. Biol. Chem., 287, 42071-42083.
38. Tammsalu,T. et al. (2014) Proteome-wide identification of SUMO2 modification sites. Sci. Signal., 7, rs2.
39. Tatham,M.H. et al. (2011) Comparative proteomic analysis identifies a role for SUMO in protein quality control. Sci. Signal., 4, rs4.
40. Teng,S. et al. (2012) Predicting protein sumoylation sites from sequence features. Amino Acids, 43, 447-455.
41. Wickham,H. (2009) ggplot2: elegant graphics for data analysis Springer New York.
42. Wilson,V.G. (2012) Sumoylation at the Host-Pathogen Interface. Biomolecules, 2, 203-227.
43. Wimmer,P. et al. (2012) Human pathogens and the host cell SUMOylation system. J. Virol., 86, 642-654.
44. Yang,S.-H. et al. (2006) An extended consensus motif enhances the specificity of substrate modification by SUMO. EMBO J., 25, 5083-5093.
45. Zhao,Q. et al. (2014) GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs. Nucleic Acids Res., 42, W325-W3230.