ASEB: a Web Server for KAT-specific Acetylation Site Prediction

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2012 May 19

PMID 22600735

Citations 43

Authors

Likun Wang

Yipeng Du

Ming Lu

Tingting Li

Affiliations

Soon will be listed here.

Abstract

Protein lysine acetylation plays an important role in the normal functioning of cells, including gene expression regulation, protein stability and metabolism regulation. Although large amounts of lysine acetylation sites have been identified via large-scale mass spectrometry or traditional experimental methods, the lysine (K)-acetyl-transferase (KAT) responsible for the acetylation of a given protein or lysine site remains largely unknown due to the experimental limitations of KAT substrate identification. Hence, the in silico prediction of KAT-specific acetylation sites may provide direction for further experiments. In our previous study, we developed the acetylation set enrichment based (ASEB) computer program to predict which KAT-families are responsible for the acetylation of a given protein or lysine site. In this article, we provide KAT-specific acetylation site prediction as a web service. This web server not only provides the online tool and R package for the method in our previous study, but several useful services are also included, such as the integration of protein-protein interaction information to enhance prediction accuracy. This web server can be freely accessed at http://cmbi.bjmu.edu.cn/huac.

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References

Spange S, Wagner T, Heinzel T, Kramer O . Acetylation of non-histone proteins modulates cellular signalling at multiple levels. Int J Biochem Cell Biol. 2008; 41(1):185-98. DOI: 10.1016/j.biocel.2008.08.027. View

Li K, Wang R, Lozada E, Fan W, Orren D, Luo J . Acetylation of WRN protein regulates its stability by inhibiting ubiquitination. PLoS One. 2010; 5(4):e10341. PMC: 2859066. DOI: 10.1371/journal.pone.0010341. View

Basu A, L Rose K, Zhang J, Beavis R, Ueberheide B, Garcia B . Proteome-wide prediction of acetylation substrates. Proc Natl Acad Sci U S A. 2009; 106(33):13785-90. PMC: 2728972. DOI: 10.1073/pnas.0906801106. View

Choudhary C, Kumar C, Gnad F, Nielsen M, Rehman M, Walther T . Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science. 2009; 325(5942):834-40. DOI: 10.1126/science.1175371. View

Li T, Du Y, Wang L, Huang L, Li W, Lu M . Characterization and prediction of lysine (K)-acetyl-transferase specific acetylation sites. Mol Cell Proteomics. 2011; 11(1):M111.011080. PMC: 3270103. DOI: 10.1074/mcp.M111.011080. View

Allfrey V, Faulkner R, Mirsky A . ACETYLATION AND METHYLATION OF HISTONES AND THEIR POSSIBLE ROLE IN THE REGULATION OF RNA SYNTHESIS. Proc Natl Acad Sci U S A. 1964; 51:786-94. PMC: 300163. DOI: 10.1073/pnas.51.5.786. View

Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P . The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2010; 39(Database issue):D561-8. PMC: 3013807. DOI: 10.1093/nar/gkq973. View

Li S, Li H, Li M, Shyr Y, Xie L, Li Y . Improved prediction of lysine acetylation by support vector machines. Protein Pept Lett. 2009; 16(8):977-83. DOI: 10.2174/092986609788923338. View

Roth S, Denu J, Allis C . Histone acetyltransferases. Annu Rev Biochem. 2001; 70:81-120. DOI: 10.1146/annurev.biochem.70.1.81. View

10.

Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T . Regulation of cellular metabolism by protein lysine acetylation. Science. 2010; 327(5968):1000-4. PMC: 3232675. DOI: 10.1126/science.1179689. View

11.

Das C, Kundu T . Transcriptional regulation by the acetylation of nonhistone proteins in humans -- a new target for therapeutics. IUBMB Life. 2005; 57(3):137-49. DOI: 10.1080/15216540500090629. View

12.

Kim S, Sprung R, Chen Y, Xu Y, Ball H, Pei J . Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell. 2006; 23(4):607-18. DOI: 10.1016/j.molcel.2006.06.026. View

13.

Cowley M, Pinese M, Kassahn K, Waddell N, Pearson J, Grimmond S . PINA v2.0: mining interactome modules. Nucleic Acids Res. 2011; 40(Database issue):D862-5. PMC: 3244997. DOI: 10.1093/nar/gkr967. View

14.

Gnad F, Ren S, Choudhary C, Cox J, Mann M . Predicting post-translational lysine acetylation using support vector machines. Bioinformatics. 2010; 26(13):1666-8. PMC: 2887055. DOI: 10.1093/bioinformatics/btq260. View

15.

Sykes S, Mellert H, Holbert M, Li K, Marmorstein R, Lane W . Acetylation of the p53 DNA-binding domain regulates apoptosis induction. Mol Cell. 2006; 24(6):841-51. PMC: 1766330. DOI: 10.1016/j.molcel.2006.11.026. View

16.

Gu W, Roeder R . Activation of p53 sequence-specific DNA binding by acetylation of the p53 C-terminal domain. Cell. 1997; 90(4):595-606. DOI: 10.1016/s0092-8674(00)80521-8. View

17.

Linding R, Jensen L, Ostheimer G, van Vugt M, Jorgensen C, Miron I . Systematic discovery of in vivo phosphorylation networks. Cell. 2007; 129(7):1415-26. PMC: 2692296. DOI: 10.1016/j.cell.2007.05.052. View

18.

Marmorstein R, Roth S . Histone acetyltransferases: function, structure, and catalysis. Curr Opin Genet Dev. 2001; 11(2):155-61. DOI: 10.1016/s0959-437x(00)00173-8. View

19.

Liu L, Scolnick D, Trievel R, Zhang H, Marmorstein R, Halazonetis T . p53 sites acetylated in vitro by PCAF and p300 are acetylated in vivo in response to DNA damage. Mol Cell Biol. 1999; 19(2):1202-9. PMC: 116049. DOI: 10.1128/MCB.19.2.1202. View

20.

Xu Y, Wang X, Ding J, Wu L, Deng N . Lysine acetylation sites prediction using an ensemble of support vector machine classifiers. J Theor Biol. 2010; 264(1):130-5. DOI: 10.1016/j.jtbi.2010.01.013. View