NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles

PLoS Computational Biology

Volumn 10, Issue 9, 2014, Pages

  Kosugi, Shunichi ^a   Yanagawa, Hiroshi ^b   Terauchi, Ryohei ^c   Tabata, Satoshi ^a  

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^b KEIO UNIVERSITY   (Japan)

^c IWATE BIOTECHNOLOGY RESEARCH CENTER   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPUTATIONAL METHODS; FORECASTING; MAMMALS;

ACCURATE PREDICTION; ACTIVITY-BASED; CARGO PROTEINS; COMPUTATIONAL TOOLS; EXPORTINS; FLANKING REGIONS; NUCLEAR EXPORT; NUCLEAR EXPORT SIGNALS; NUCLEAR IMPORT; SPECIFIC RECOGNITION;

PROTEINS;

GREEN FLUORESCENT PROTEIN; KARYOPHERIN; LEUCINE; NUCLEAR EXPORT SIGNAL;

ACCURACY; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; COMPUTER ANALYSIS; CONTROLLED STUDY; DNA FLANKING REGION; ENZYME REGULATION; FALSE POSITIVE RESULT; HYDROPHOBICITY; MATHEMATICAL COMPUTING; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEAR EXPORT SIGNAL; PREDICTION; PROCESS OPTIMIZATION; PROTEIN MOTIF; 3T3 CELL LINE; ACTIVE TRANSPORT; ANIMAL; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; GENETICS; MOLECULAR GENETICS; MOUSE; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROCEDURES; RECEIVER OPERATING CHARACTERISTIC; SEQUENCE ANALYSIS;

ACTIVE TRANSPORT, CELL NUCLEUS; AMINO ACID SEQUENCE; ANIMALS; COMPUTATIONAL BIOLOGY; DNA MUTATIONAL ANALYSIS; LEUCINE; MICE; MOLECULAR SEQUENCE DATA; NIH 3T3 CELLS; NUCLEAR EXPORT SIGNALS; ROC CURVE; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84907584432     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003841     Document Type: Article

References (29)

1. Ossareh-Nazari B, Gwizdek C, Dargemont C, (2001) Protein export from the nucleus. Traffic 2: 684–689.
2. Fornerod M, Ohno M, (2002) Exportin-mediated nuclear export of proteins and ribonucleoproteins. Results Probl Cell Differ 35: 67–91.
3. Pemberton LF, Paschal BM, (2005) Mechanisms of receptor-mediated nuclear import and nuclear export. Traffic 6: 187–198.
4. Kudo N, Matsumori N, Taoka H, Fujiwara D, Schreiner EP, et al. (1999) Leptomycin B inactivates CRM1/exportin 1 by covalent modification at a cysteine residue in the central conserved region. Proc Natl Acad Sci U S A 96: 9112–9117.
5. Fu SC, Huang HC, Horton P, Juan HF, (2013) ValidNESs: a database of validated leucine-rich nuclear export signals. Nucleic Acids Res 41: D338–343.
6. Matsuyama A, Arai R, Yashiroda Y, Shirai A, Kamata A, et al. (2006) ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. Nat Biotechnol 24: 841–847.
7. Thakar K, Karaca S, Port SA, Urlaub H, Kehlenbach RH, (2013) Identification of CRM1-dependent Nuclear Export Cargos Using Quantitative Mass Spectrometry. Mol Cell Proteomics 12: 664–678.
8. Nguyen KT, Holloway MP, Altura RA, (2012) The CRM1 nuclear export protein in normal development and disease. Int J Biochem Mol Biol 3: 137–151.
9. Turner JG, Dawson J, Sullivan DM, (2012) Nuclear export of proteins and drug resistance in cancer. Biochem Pharmacol 83: 1021–1032.
10. Bogerd HP, Fridell RA, Benson RE, Hua J, Cullen BR, (1996) Protein sequence requirements for function of the human T-cell leukemia virus type 1 Rex nuclear export signal delineated by a novel in vivo randomization-selection assay. Mol Cell Biol 16: 4207–4214.
11. Zhang MJ, Dayton AI, (1998) Tolerance of diverse amino acid substitutions at conserved positions in the nuclear export signal (NES) of HIV-1 Rev. Biochem Biophys Res Commun 243: 113–116.
12. Henderson BR, Eleftheriou A, (2000) A comparison of the activity, sequence specificity, and CRM1-dependence of different nuclear export signals. Exp Cell Res 256: 213–224.
13. la Cour T, Kiemer L, Molgaard A, Gupta R, Skriver K, et al. (2004) Analysis and prediction of leucine-rich nuclear export signals. Protein Eng Des Sel 17: 527–536.
14. Kosugi S, Hasebe M, Tomita M, Yanagawa H, (2008) Nuclear export signal consensus sequences defined using a localization-based yeast selection system. Traffic 9: 2053–2062.
15. Xu D, Farmer A, Collett G, Grishin NV, Chook YM, (2012) Sequence and structural analyses of nuclear export signals in the NESdb database. Mol Biol Cell 23: 3677–3693.
16. Güttler T, Madl T, Neumann P, Deichsel D, Corsini L, et al. (2010) NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1. Nat Struct Mol Biol 17: 1367–1376.
17. Monecke T, Güttler T, Neumann P, Dickmanns A, Görlich D, et al. (2009) Crystal structure of the nuclear export receptor CRM1 in complex with Snurportin1 and RanGTP. Science 324: 1087–1091.
18. Dong X, Biswas A, Chook YM, (2009) Structural basis for assembly and disassembly of the CRM1 nuclear export complex. Nat Struct Mol Biol 16: 558–560.
19. Dong X, Biswas A, Suel KE, Jackson LK, Martinez R, et al. (2009) Structural basis for leucine-rich nuclear export signal recognition by CRM1. Nature 458: 1136–1141.
20. la Cour T, Gupta R, Rapacki K, Skriver K, Poulsen FM, et al. (2003) NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Res 31: 393–396.
21. Fu SC, Imai K, Horton P, (2011) Prediction of leucine-rich nuclear export signal containing proteins with NESsential. Nucleic Acids Res 39: e111.
22. Diella F, Haslam N, Chica C, Budd A, Michael S, et al. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13: 6580–6603.
23. Prieto G, Fullaondo A, Rodriguez JA, (2014) Prediction of nuclear export signals using weighted regular expressions (Wregex). Bioinformatics 30: 1220–7.
24. Bailey TL, Elkan C, (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28–36.
25. Obenauer JC, Cantley LC, Yaffe MB, (2003) Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 31: 3635–3641.
26. Garcia-Santisteban I, Banuelos S, Rodriguez JA, (2012) A global survey of CRM1-dependent nuclear export sequences in the human deubiquitinase family. Biochem J 441: 209–217.
27. Kosugi S, Hasebe M, Tomita M, Yanagawa H, (2009) Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs. Proc Natl Acad Sci U S A 106: 10171–10176.
28. Wen W, Meinkoth JL, Tsien RY, Taylor SS, (1995) Identification of a signal for rapid export of proteins from the nucleus. Cell 82: 463–473.
29. Kosugi S, Hasebe M, Matsumura N, Takashima H, Miyamoto-Sato E, et al. (2009) Six classes of nuclear localization signals specific to different binding grooves of importin alpha. J Biol Chem 284: 478–485.