Architecture, function and prediction of long signal peptides

Briefings in Bioinformatics

Volumn 10, Issue 5, 2009, Pages 569-578

  Hiss, Jan A ^a   Schneider, Gisbert ^a  

^a GOETHE UNIVERSITY   (Germany)

Author keywords

Bioinformatics; Machine learning; Organelle; Protein targeting; Signal sequence; Transit peptide

Indexed keywords

SIGNAL PEPTIDE;

ALGORITHM; AMINO TERMINAL SEQUENCE; CELL MATURATION; CELL SURVIVAL; COMPUTER PREDICTION; COMPUTER PROGRAM; ENDOPLASMIC RETICULUM; EUKARYOTIC CELL; INTRACELLULAR MEMBRANE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TARGETING; PROTEIN TRANSPORT; REVIEW;

AMINO ACID SEQUENCE; ANIMALS; COMPUTATIONAL BIOLOGY; ENDOPLASMIC RETICULUM; HUMANS; MOLECULAR SEQUENCE DATA; PROTEIN SORTING SIGNALS; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ANALYSIS, PROTEIN;

EUKARYOTA;

EID: 69249124625     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbp030     Document Type: Review

References (64)

1. Blobel G, Dobberstein B. Transfer of proteins across membranes. I. Presence of proteolytically processed and unprocessed nascent immunoglobulin light chains on membrane-bound ribosomes of murine myeloma. J Cell Biol 1975;67:835-51.
2. Blobel G, Dobberstein B. Transfer of proteins across membranes. II. Reconstitution of functional rough microsomes from heterologous components. J Cell Biol 1975;67: 852-62.
3. Gierasch LM. Signal Sequences. Biochemistry 1989;28: 923-30.
4. Pugsley AP. Translocation of proteins with signal sequences across membranes. Curr Opin Cell Biol 1990;2:609-16.
5. Bendtsen JD, Nielsen H, von Heijne G, et al. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004; 340:783-95.
6. Schneider G, Fechner U. Advances in the prediction of protein targeting signals. Proteomics 2004;4:1571-80.
7. von Heijne G. Signal sequences. The limits of variation. J Mol Biol 1985;184:99-105.
8. von Heijne G. Patterns of amino acids near signal-sequence cleavage sites. Eur J Biochem 1983;133:17-21.
9. Siegel V, Walter P. Each of the activities of signal recognition particle (SRP) is contained within a distinct domain: Analysis of biochemical mutants of SRP. Cell 1988;52: 39-49.
10. Wolin SL, Walter P. Discrete nascent chain lengths are required for the insertion of presecretory proteins into microsomal membranes. J Cell Biol 1993;121:1211-19.
11. Gilmore R, Walter P, Blobel G. Protein translocation across the endoplasmic reticulum. II. Isolation and characterization of the signal recognition particle receptor. J Cell Biol 1982;95:470-77.
12. Deshaies RJ, Sanders SL, Feldheim DA, et al. Assembly of yeast Sec proteins involved in translocation into the endoplasmic reticulum into a membrane-bound multisubunit complex. Nature 1991;349:806-08.
13. Kalies KU, Stokes V, Hartmann E. A single Sec61-complex functions as a protein-conducting channel. Biochim Biophys Acta 2008;1783 2375-83.
14. Görlich D, Hartmann E, Prehn S, et al. A protein of the endoplasmic reticulum involved early in polypeptide translocation. Nature 1992;357:47-52.
15. Walter P. Protein translocation. Travelling by TRAM. Nature 1992;357:22-3.
16. Voigt S, Jungnickel B, Hartmann E, et al. Signal sequence-dependent function of the TRAM protein during early phases of protein transport across the endoplasmic reticulum membrane. J Cell Biol 1996;134:25-35.
17. Fons RD, Bogert BA. Hegde RS Substrate-specific function of the translocon-associated protein complex during translocation across the ER membrane. J Cell Biol 2008;160: 529-39.
18. Ménétret JF, Hegde RS, Aguiar M, et al. Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome. Structure 2008;16:1126-37.
19. Siegel V. A second signal recognition event required for translocation into the endoplasmic reticulum. Cell 1995; 82:167-70.
20. Hoyt DW, Gierasch LM. Hydrophobic content and lipid interactions of wild-type and mutant OmpA signal peptides correlate with their in vivo function. Biochemistry 1991; 30: 10155-63.
21. Hoyt DW, Gierasch LM. A peptide corresponding to an export-defective mutant OmpA signal sequence with asparagine in the hydrophobic core is unable to insert into model membranes. J Biol Chem 1991;266 14406-12.
22. Jungnickel B, Rapoport TA. A posttargeting signal sequence recognition event in the endoplasmic reticulum membrane. Cell 1995;82 261-270.
23. Rapoport TA. Protein transport across the endoplasmic reticulum membrane. FEBS J 2008;275:4471-78.
24. Evans EA, Gilmore R, Blobel G. Purification of microsomal signal peptidase as a complex. Proc Natl Acad Sci USA 1986; 83 581-85.
25. Weihofen A, Binns K, Lemberg MK, et al. Identification of signal peptide peptidase, a presenilin-type aspartic protease. Science 2002;296:2215-8.
26. Hegde RS. Targeting and beyond: New roles for old signal sequences. Mol Cell 2002;10:697-8.
27. Lemberg MK, Martoglio B. Requirements for signal peptide peptidase-catalyzed intramembrane proteolysis. Mol Cell 2002;10 735-44.
28. Klappa P, Dierks T, Zimmermann R. Cyclosporin A inhibits the degradation of signal sequences after processing of presecretory proteins by signal peptidase. Eur J Biochem 1996;239:509-18.
29. Ulbrecht M, Martinozzi S, Grzeschik M, et al. Cutting edge: The human cytomegalovirus UL40 gene product contains a ligand for HLA-E and prevents NK cell-mediated lysis. J Immunol 2000;164:5019-22.
30. Stangl S, Gross C, Pockley AG. Influence of Hsp70 and HLA-E on the killing of leukemic blasts by cytokine/Hsp70 peptide-activated human natural killer (NK) cells. Cell Stress Chaperones 2008;13 221-30.
31. Eichler R, Lenz O, Strecker T, et al. Identification of Lassa virus glycoprotein signal peptide as a trans-acting maturation factor. EMBO Rep 2003;4:1084-8.
32. Eichler R, Lenz O, Strecker T, Garten W. Signal peptide of Lassa virus glycoprotein GP-C exhibits an unusual length. FEBS Lett 2003; 538:203-6.
33. Schrempf S, Froeschke M, Giroglou T, et al. Signal peptide requirements for lymphocytic choriomeningitis virus glycoprotein C maturation and virus infectivity. J Virol 2007;81:12515-24.
34. Dultz E, Hildenbeutel M, Martoglio B, et al. The signal peptide of the mouse mammary tumor virus Rem protein is released from the endoplasmic reticulum membrane and accumulates in nucleoli. J Biol Chem 2008;283: 9966-76.
35. Kurys G, Tagaya Y, Bamford R, et al. The Long Signal Peptide Isoform and Its Alternative Processing Direct the Intracellular Trafficking of Interleukin-15. J Biol Chem 2000; 275:30653-9.
36. Ogata RT, Mathias P, Bradt BM, Cooper NR. Murine C4b-binding protein. Mapping of the ligand binding site and the N-terminus of the pre-protein. J Immunol 1993;150: 2273-80.
37. Wu CH, Apweiler R, Bairoch A, et al. The Universal Protein Resource (UniProtKB): An expanding universe of protein information. Nucleic Acids Res 2006;34:D187-91.
38. Emanuelsson O, Nielsen H, Brunak B, et al. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 2000;300: 1005-16.
39. von Messling V, Cattaneo R. Amino-terminal precursor sequence modulates canine distemper virus fusion protein function. J Virol 2002;76 4172-80.
40. Meissner M, Koch O, Klebe G, Schneider G. Prediction of turn types in protein structure by machine-learning classifiers. Proteins 2009;74:344-52.
41. Hiss JA, Resch E, Schreiner A, et al. Domain organization of long signal peptides of single-pass integral membrane proteins reveals multiple functional capacity. PLoS One 2008;3:e2767.
42. Peeters N, Small I. Dual targeting to mitochondria and chloroplasts. Biochim Biophys Acta 2001;1541:54-63.
43. Bhushan S, Lefebvre B, Stähl A, et al. Dual targeting and function of a protease in mitochondria and chloroplasts. EMBO Rep 2003;4:1073-8.
44. Silvia-Filho MC. One ticket for multiple destinations: Dual targeting of proteins to distinct subcellular locations. Curr Opin Plant Biol 2003;6:589-95.
45. Hansson CA, Frykman S, Farmery MR, et al. Nicastrin, presenilin, APH-1, and PEN-2 form active gammasecretase complexes in mitochondria. J Biol Chem 2004; 279:51654-60.
46. Anandatheerthavarada HK, Biswas G, Mullick J, et al. Dual targeting of cytochrome P4502B1 to endoplasmic reticulum and mitochondria involves a novel signal activation by cyclic AMP-dependent phosphorylation at ser128. EMBO J 1999;18:5494-504.
47. Käll L, Krogh A, Sonnhammer EL. Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. Nucleic Acids Res 2007;35: W429-32.
48. Resch E, Quaiser S, Quaiser T, et al. Synergism of shrew-1's signal peptide and transmembrane segment required for plasma membrane localization. Traffic 2008;9: 1344-53.
49. Reynolds SM, Käll L, Riffle ME, et al. Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput Biol 2008;4:e1000213.
50. Hiller K, Grote A, Scheer M, et al. PrediSi prediction of signal peptides and their cleavage positions. Nucleic Acids Res 2004; 32(Web Server Issue):W375-9.
51. Chou KC, Shen HB. Signal-CF a subsite-coupled and window-fusing approach for predicting signal peptides. Biochem Biophys Res Commun 2007; 357:633-40.
52. Shen HB, Chou KC. Signal-3L A 3-layer approach for predicting signal peptides. Biochem Biophys Res Commun 2007;363:297-303.
53. Horton P, Park KJ, Obayashi T, et al. WoLF PSOR T: Protein localization predictor. Nucleic Acids Res 2007; 35(Web Server Issue):W585-7.
54. Viklund H, Bernsel A, Skwark M, et al. SPOCTOPUS: A combined predictor of signal peptides and membrane protein topology. Bioinformatics 2008;24:2928-9.
55. Rassokhin DN, Agrafiotis DK. Kolmogorov-Smirnov statistic and its application in library design. J Mol Graphics Model 2000;18 368-82.
56. Hegde RS, Bernstein HD. The surprising complexity of signal sequences. Trends Biochem Sci 2006;31:563-71.
57. Kim SJ, Rahbar R, Hegde RS. Combinatorial control of prion protein biogenesis by the signal sequence and transmembrane domain. J Biol Chem 2001;276:26132-40.
58. Kim SJ, Hegde RS. Cotranslational partitioning of nascent prion protein into multiple populations at the translocation channel. Mol Biol Cell 2002;13:3775-86.
59. Kee KS, Jois SD. Design of beta-turn based therapeutic agents. Curr Pharm Des 2003;9:1209-24.
60. Hershberger SJ, Lee SG, Chmielewski J. Scaffolds for blocking protein-protein interactions. Curr Top Med Chem 2007;7: 928-42.
61. Dowd CS, Leavitt S, Babcock G, et al. Beta-turn Phe in HIV-1 Env binding site of CD4 and CD4 mimetic miniprotein enhances Env binding affinity but is not required for activation of co-receptor/17b site. Biochemistry 2002;41:7038-46.
62. Kaderbhai MA, Morgan R, Kaderbhai NN. The membrane-interactive tail of cytochrome b(5) can function as a stop-transfer sequence in concert with a signal sequence to give inversion of protein topology in the endoplasmic reticulum. Arch Biochem Biophys 2003;412:259-66.
63. Park S, Liu G, Topping TB, et al. Modulation of folding pathways of exported proteins by the leader sequence. Science 1989;239 1033-5.
64. Liu G, Topping TB, Randall LL. Physiological role during export for the retardation of folding by the leader peptide of maltose-binding protein. Proc Natl Acad Sci USA 1989;86: 9213-7.