Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units

PLoS Genetics

Volumn 2, Issue 4, 2006, Pages 554-563

  Davis, Melissa J ^a   Hanson, Kelly A ^a   Clark, Francis ^a   Fink, J Lynn ^a   Zhang, Fasheng ^a   Kasukawa, Takeya ^b   Kai, Chikatoshi ^b   Kawai, Jun ^b,c   Carninci, Piero ^b,c   Hayashizaki, Yoshihide ^b,c   Teasdale, Rohan D ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

^c Japan Science and Technology Agency   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ISOPROTEIN; MEMBRANE PROTEIN; SIGNAL PEPTIDE; TRANSCRIPTOME;

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; ARTICLE; GENETIC TRANSCRIPTION; MEMBRANE STRUCTURE; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN VARIANT; ANIMAL; GENETIC VARIABILITY; GENETICS;

ANIMALS; MEMBRANE PROTEINS; PROTEIN ISOFORMS; PROTEIN SORTING SIGNALS; TRANSCRIPTION, GENETIC; VARIATION (GENETICS);

EID: 33646466927     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0020046     Document Type: Article

References (57)

1. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al. (2005) The transcriptional landscape of the mammalian genome. Science 309: 1159-1563.
2. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563-573.
3. Modrek B, Lee C (2002) A genomic view of alternative splicing. Nat Genet 30: 13-19.
4. Matlin AJ, Clark F, Smith CWJ (2005) Understanding alternative splicing: Towards a cellular splicing code. Nat Rev Mol Cell Biol 6: 386-398.
5. Stamm S, Ben-Ari S, Rafalska I, Tang Y, Zhang Z, et al. (2005) Function of alternative splicing. Gene 344: 1-20.
6. Xing Y, Xu Q, Lee C (2003) Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains. FEBS Lett 555: 572-578.
7. Martoglio B, Dobberstein B (1998) Signal sequences: More than just greasy peptides. Trends Cell Biol 8: 410-415.
8. Sakaguchi M (2002) Autonomous and heteronomous positioning of transmembrane segments in multispanning membrane protein. Biochem Biophys Res Commun 296: 1-4.
9. Yuan Z, Davis MJ, Zhang F, Teasdale RD (2003) Computational differentiation of N-terminal signal peptides and transmembrane domains. Biochem Biophys Res Commun 312: 1278-1283.
10. Kanapin A, Batalov S, Davis MJ, Gough J, Grimmond SM, et al. (2003) Mouse proteome analysis. Genome Res 13: 1335-1344.
11. Clark F, Thanaraj TA (2002) Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human. Hum Mol Genet 11: 451-464.
12. Mayer RJ (2000) The meteoric rise of regulated intracellular proteolysis. Nat Rev Mol Cell Biol 1: 145-148.
13. Arribas J, Borroto A (2002) Protein ectodomain shedding. Chem Rev 102: 4627-4637.
14. Cline MS, Shigeta R, Wheeler RL, Siani-Rose MA, Kulp D, et al. (2004) The effects of alternative splicing on transmembrane proteins in the mouse genome. Pac Symp Biocomput 2004: 17-28.
15. Moller S, Mix E, Bluggel M, Serrano-Fernandez P, Koczan D, et al. (2005) Collection of soluble variants of membrane proteins for transcriptomics and proteomics. In Silico Biol 5: 295-311.
16. Aturaliya RN, Fink JL, Davis MJ, Teasdale MS, Hanson KA, et al. (2006) Subcellular localization of mammalian type II membrane proteins. Traffic. In press.
17. Thanaraj TA, Stamm S, Clark F, Riethoven JJ, Le Texier V, et al. (2004) ASD: The Alternative Splicing Database. Nucleic Acids Res 32: 64-69.
18. Takematsu H, Diaz S, Stoddart A, Zhang Y, Varki A (1999) Lysosomal and cytosolic sialic acid 9-O-acetylesterase activities can be encoded by one gene via differential usage of a signal peptide-encoding exon at the N terminus. J Biol Chem 274: 25623-25631.
19. Wabakken T, Hauge H, Funderud S, Aasheim HC (2002) Characterization, expression and functional aspects of a novel protein tyrosine phosphatase epsilon isoform. Scand J Immunol 56: 276-285.
20. Gillingham AK, Pfeifer AC, Munro S (2002) CASP, the alternatively spliced product of the gene encoding the CCAAT-displacement protein transcription factor, is a Golgi membrane protein related to giantin. Mol Biol Cell 11: 3761-3774.
21. Pixley FJ, Lee PS, Dominguez MG, Einstein DB, Stanley ER (1995) A heteromorphic protein-tyrosine phosphatase, PTP phi, is regulated by CSF-1 in macrophages. J Biol Chem 270: 27339-27347.
22. Fang W, Rivard JJ, Mueller DL, Behrens TW (1994) Cloning and molecular characterization of mouse bcl-x in B and T lymphocytes. J Immunol 153: 4388-4398.
23. Clark RM, Marker PC, Kingsley DM (2000) A novel candidate gene for mouse and human reaxial polydactyly with altered expression in limbs of Heminelic extra-toes mutant mice. Genomics 67: 19-27.
24. Kruse S, Forster J, Kuehr J, Deichmann KA (1999) Characterization of the membrane-bound and soluble form of human IL-4 receptor alpha produced by alternative splicing. Int Immunol 11: 1965-1970.
25. Tone M, Tone Y, Fairchild PJ, Wykes M, Waldmann H (2001) Regulation of CD40 function by its isoforms generated through alternative splicing. Proc Natl Acad Sci U S A 98: 1751-1756.
26. Bernard DJ, Woodruff TK (2001) Inhibin binding protein in rats: Alternative transcripts and regulation in the pituitary across the estrous cycle. Mol Endocrinol 15: 654-667.
27. Nakamura F, Goshima Y (2002) Structural and functional relation of neurophilins. Adv Exp Med Biol 515: 55-69.
28. Reiter JL, Maihle NJ (2003) Characterization and expression of novel 60-kDa and 110-kDa EGFR isoforms in human placenta. Ann N Y Acad Sci 995: 39-47.
29. Huckle WR, Roche RI (2004) Post-transcriptional control of expression of sFlt-1, an endogenous inhibitor of vascular endothelial growth factor. J Cell Biochem 93: 120-132.
30. Raines MA, Liu L, Quan SG, Joe V, DiPersio JF, et al. (1991) Identification and molecular cloning of a soluble human granulocyte-macrophage colony-stimulating factor receptor. Proc Natl Acad Sci U S A 88: 8203-8207.
31. Setareh M, Schwarz H, Lotz M (1995) A mRNA variant encoding a soluble form of 4-1BB, a member of the murine NGF/TNF receptor family. Gene 164: 311-315.
32. Lyman SD, James L, Escobar S, Downey H, de Vries P, et al. (1995) Identification of soluble and membrane-bound isoforms of the murine flt3 ligand generated by alternative splicing of mRNAs. Oncogene 10: 149-157.
33. Bergers G, Reikerstorfer A, Braselmann S, Graniger P, Busslinger M (1994) Alternative promoter usage of the Fos-responsive gene Fit-1 generates mRNA isoforms coding for either secreted or membrane-bound proteins related to the IL-1 receptor. EMBO J 13: 1176-1188.
34. Horiuchi S, Koyanagi Y, Tanaka Y, Waki M, Matsumoto A, et al. (1997) Altered interleukin-2 receptor alpha-chain is expressed in human T-cell leukaemia virus type-I-infected T-cell lines and human peripheral blood mononuclear cells of adult T-cell leukaemia patients through an alternative splicing mechanism. Immunology 91: 28-34.
35. Gavrilova O, Barr V, Marcus-Samuels B, Rietman M (1997) Hyperleptinemia of pregnancy associated with the appearance of a circulating form of the leptin receptor. J Biol Chem 272: 30546-30551.
36. Takeshita A (1994) An alternatively spliced form of the human thyrotropin receptor transcript. Nippon Rinsho 52: 974-978.
37. Van den Maagdenberg AM, Bachner D, Schepens JT, Peters W, Fransen JA, et al. (1999) The mouse Ptprr gene encodes two protein tyrosine phosphatases, PTP-SL and PTPBR7, that display distinct patterns of expression during neural development. Eur J Neurosci 11: 3832-3844.
38. Ma T, Yang B, Verkman AS (1996) Gene structure, cDNA cloning and expression of a mouse mercurial-insensitive water channel. Genomics 33: 382-388.
39. Delaney SJ, Rich DP, Thomson SA, Hargrave MR, Lovelock PK, et al. (1993) Cystic fibrosis transmembrane conductance regulator splice variants are not conserved and fail to produce chloride channels. Nat Genet 4: 426-431.
40. Tanaka K, Okabayashi K, Asashima M, Perrimon N, Kadowaki T (2000) The evolutionarily conserved porcupine gene family is involved in the processing of the Wnt family. Eur J Biochem 267: 4300-4311.
41. Nash SR, Giros B, Kingsmore SF, Kim KM, el-Mestikawy S, et al. (1998) Cloning, gene structure and genomic localization of an orphan transporter from mouse kidney with six alternatively-spliced isoforms. Receptors Channels 6: 113-128.
42. Karakashian A, Timmer RT, Klein JD, Gunn RB, Sands JM, et al. (1999) Cloning and characterization of two new isoforms of the rat kidney urea transporter: UT-A3 and UT0A4. J Am Soc Nephrol 10: 230-237.
43. Verboomen H, Wuytak F, Van den Bosch L, Mertens L, Casteels R (1994) The functional importance of the extreme C-terminal tail in the gene 2 organellar Ca(2+)-transport ATPase (SERCA2a/b). Biochem J 303: 979-984.
44. Fink JL, Aturaliya RN, Davis MJ, Hanson KA, Teasdale MS, et al. (2006) LOCATE: A protein subcellular localization database. Nucleic Acids Res 34: 213-217.
45. Bertaccini E, Trudell JR (2002) Predicting the transmembrane secondary structure of ligand-gated ion channels. Protein Eng 15: 443-453.
46. Yuan Z, Mattick JS, Teasdale RD (2004) SVMtm: Support vector machines to predict transmembrane segments. J Comput Chem 25: 632-636.
47. Krogh A, Larsson B, vonHeijne G, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol 305: 567-580.
48. Tusnady GE, Simon I (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17: 849-850.
49. Jones DT, Taylor WR, Thornton JM (1994) A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33: 3038-3049.
50. Cserzo M, Wallin E, Simon I, vonHeijne G, Elofsson A (1997) Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: The dense alignment surface method. Protein Eng 10: 673-676.
51. vonHeijne G (1986) A new method for predicting signal sequence cleavage sites. Nucleic Acids Res 11: 4683-4690.
52. Nielsen H, Engelbrecht J, Brunak S, vonHeijne G (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 10: 1-6.
53. Nielsen H, Krogh A (1998) Prediction of signal peptides and signal anchors by a hidden Markov model. In: Glasgow J, Littlejohn T, Major F, Lathrop R, Sankoff D, et al., editors. Proceedings of the Sixth International Conference on Intelligence Systems for Molecular Biology. Menlo Park (California): AAAI Press. pp. 122-130.
54. Lee BTK, Tan TW, Ranganathan S (2004) DEDB: A database of Drosophila melanogaster exons in splicing graph form. BMC Bioinformatics 5: D59-D63.
55. Blake JA, Richardson JE, Bult CJ, Kadin JA, Eppig JT (2003) MGD: The Mouse Genome Database. Nucleic Acids Res 31: 193-195.
56. Eppig JT, Blake JA, Burkhart DL, Goldsmith CW, Lutz CM, et al. (2002) Corralling conditional mutations: A unified resource for mouse phenotypes. Genesis 32: 63-65.
57. Beissbarth T, Speed TP (2004) GOstat: Find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20: 1464-1465.