Prediction of twin-arginine signal peptides

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Bendtsen, Jannick Dyrløv ^a   Nielsen, Henrik ^a   Widdick, David ^b,c   Palmer, Tracy ^b,c   Brunak, Søren ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b JOHN INNES CENTRE   (United Kingdom)

^c UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CLEAVAGE SITES; CYTOPLASMIC PROTEINS; EXTRACELLULAR ENVIRONMENTS; INPUT SEQUENCE; PREDICTION METHODS; REGULAR EXPRESSIONS; TAT SIGNAL PEPTIDE; TRANSLOCATION PATHWAY;

ARGININE; FORECASTING; NEURAL NETWORKS; PATTERN MATCHING; PROTEINS;

GENE ENCODING;

ARGININE; BACTERIAL PROTEIN; CYTOPLASM PROTEIN; SIGNAL PEPTIDE; CARRIER PROTEIN;

ACCURACY; ANALYTIC METHOD; ARTICLE; ARTIFICIAL NEURAL NETWORK; CLASSIFICATION; COMPUTER LANGUAGE; CONTROLLED STUDY; HYDROPHOBICITY; INTERNET; MATHEMATICAL COMPUTING; NONHUMAN; PEPTIDE ANALYSIS; PREDICTION; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN MOTIF; SEQUENCE ANALYSIS; ISOLATION AND PURIFICATION; METABOLISM; PROCEDURES;

BACTERIA (MICROORGANISMS);

ARGININE; BACTERIAL PROTEINS; MEMBRANE TRANSPORT PROTEINS; NEURAL NETWORKS (COMPUTER); PROTEIN SORTING SIGNALS; SEQUENCE ANALYSIS, PROTEIN;

EID: 25444441166     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-167     Document Type: Article

References (29)

1. Berks BC: A common export pathway for proteins binding complex redox cofactors? Mol Microbiol 1996, 22(3):393-404.
2. Sargent F, Bogsch EG, Stanley NR, Wexler M, Robinson C, Berks BC, Palmer T: Overlapping functions of components of a bacterial Sec-independent protein export pathway. Embo J 1998, 17(13):3640-3650.
3. Weiner JH, Bilous PT, Shaw GM, Lubitz SP, Frost L, Thomas GH, Cole JA, Turner RJ: A novel and ubiquitous system for membrane targeting and secretion of cofactor-containing proteins. Cell 1998, 93(1):93-101.
4. Berks BC, Palmer T, Sargent F: The Tat protein translocation pathway and its role in microbial physiology. Adv Microb Physiol 2003, 47:187-254.
5. DeLisa MP, Tullman D, Georgiou G: Folding quality control in the export of proteins by the bacterial twin-arginine translocation pathway. Proc Natl Acad Sci U S A 2003, 100(10):6115-6120.
6. Musser SM, Theg SM: Characterization of the early steps of OE17 precursor transport by the thylakoid DeltapH/Tat machinery. Eur J Biochem 2000, 267(9):2588-2598.
7. Yahr TL, Wickner WT: Functional reconstitution of bacterial Tat translocation in vitro. Embo J 2001, 20(10):2472-2479.
8. Cristobal S, de Gier JW, Nielsen H, von Heijne G: Competition between Sec- and TAT-dependent protein translocation in Escherichia coli. Embo J 1999, 18(11):2982-2990.
9. Rose RW, Bruser T, Kissinger JC, Pohlschroder M: Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway. Mol Microbiol 2002, 45(4):943-950.
10. Chaddock AM, Mant A, Karnauchov I, Brink S, Herrmann RG, Klosgen RB, Robinson C: A new type of signal peptide: central role of a twin-arginine motif in transfer signals for the delta pH-dependent thylakoidal protein translocase. Embo J 1995, 14(12):2715-2722.
11. Hinsley AP, Stanley NR, Palmer T, Berks BC: A naturally occurring bacterial Tat signal peptide lacking one of the 'invariant' arginine residues of the consensus targeting motif. FEBS Lett 2001, 497(1):45-49.
12. Ignatova Z, Hornle C, Nurk A, Kasche V: Unusual signal peptide directs penicillin amidase from Escherichia coli to the Tat translocation machinery. Biochem Biophys Res Commun 2002, 291(1):146-149.
13. Stanley NR, Palmer T, Berks BC: The twin arginine consensus motif of Tat signal peptides is involved in Sec-independent protein targeting in Escherichia coli. J Biol Chem 2000, 275(16):11591-11596.
14. Ize B, Gerard F, Zhang M, Chanal A, Voulhoux R, Palmer T, Filloux A, Wu LF: In vivo dissection of the Tat translocation pathway in Escherichia coli. J Mol Biol 2002, 317(3):327-335.
15. Buchanan G, Sargent F, Berks BC, Palmer T: A genetic screen for suppressors of Escherichia coli Tat signal peptide mutations establishes a critical role for the second arginine within the twin-arginine motif. Arch Microbiol 2001, 177(1):107-112.
16. DeLisa MP, Samuelson P, Palmer T, Georgiou G: Genetic analysis of the twin arginine translocator secretion pathway in bacteria. J Biol Chem 2002, 277(33):29825-29831.
17. Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340(4):783-795.
18. Nielsen H, Engelbrecht J, Brunak S, von Heijne G: Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 1997, 10(1):1-6.
19. Bowers CW, Lau F, Silhavy TJ: Secretion of LamB-LacZ by the signal recognition particle pathway of Escherichia coli. J Bacteriol 2003, 185(19):5697-5705.
20. Lee HC, Bernstein HD: The targeting pathway of Escherichia coli presecretory and integral membrane proteins is specified by the hydrophobicity of the targeting signal. Proc Natl Acad Sci U S A 2001, 98(6):3471-3476.
21. Dilks K, Rose RW, Hartmann E, Pohlschroder M: Prokaryotic utilization of the twin-arginine translocation pathway: a genomic survey. J Bacteriol 2003, 185(4):1478-1483.
22. Bairoch A, Apweiler R: The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2000, 28(1):45-48.
23. Nielsen H, Engelbrecht J, Brunak S, von Heijne G: A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int J Neural Syst 1997, 8(5-6):581-599.
24. Jongbloed JD, Antelmann H, Hecker M, Nijland R, Bron S, Airaksinen U, Pries F, Quax WJ, van Dijl JM, Braun PG: Selective contribution of the twin-arginine translocation pathway to protein secretion in Bacillus subtilis. J Biol Chem 2002, 277(46):44068-44078.
25. Jongbloed JD, Grieger U, Antelmann H, Hecker M, Nijland R, Bron S, van Dijl JM: Two minimal Tat translocases in Bacillus. Mol Microbiol 2004, 54(5):1319-1325.
26. Gafvelin G, Sakaguchi M, Andersson H, von Heijne G: Topological rules for membrane protein assembly in eukaryotic cells. J Biol Chem 1997, 272(10):6119-6127.
27. Molik S, Karnauchov I, Weidlich C, Herrmann RG, Klosgen RB: The Rieske Fe/S protein of the cytochrome b6/f complex in chloroplasts: missing link in the evolution of protein transport pathways in chloroplasts? J Biol Chem 2001, 276(46):42761-42766.
28. Stanley NR, Sargent F, Buchanan G, Shi J, Stewart V, Palmer T, Berks BC: Behaviour of topological marker proteins targeted to the Tat protein transport pathway. Mol Microbiol 2002, 43(4):1005-1021.
29. Schneider TD, Stephens RM: Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 1990, 18(20):6097-6100.