Bioinformatic identification of polymerizing and transmembrane mucins in the puffer fish Fugu rubripes

Glycobiology

Volumn 14, Issue 6, 2004, Pages 521-527

  Lang, Tiange ^a   Alexandersson, Marina ^b   Hansson, Gunnar C ^a   Samuelsson, Tore ^a  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b FRAUNHOFER CHALMERS CENTRE   (Sweden)

Author keywords

Bioinformatics; EGF; Glycosylation; Mucin; SEA

Indexed keywords

AMINO ACID; GLYCOPROTEIN; MEMBRANE PROTEIN; MUCIN; MUCIN 2;

AMINO ACID COMPOSITION; ARTICLE; BIOINFORMATICS; GEL; GENETIC CONSERVATION; MAMMAL; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN POLYMERIZATION; PUFFER FISH; VERTEBRATE;

ANIMALS; BIOPOLYMERS; COMPUTATIONAL BIOLOGY; MEMBRANE PROTEINS; MUCINS; TAKIFUGU;

MAMMALIA; TAKIFUGU; TAKIFUGU RUBRIPES; TETRAODONTIDAE; VERTEBRATA;

EID: 3042842452     PISSN: 09596658     EISSN: None     Source Type: Journal    
DOI: 10.1093/glycob/cwh066     Document Type: Article

References (21)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acid Res., 25, 3389-3402.
2. Aparicio, S., Chapman, J., and Brenner, S. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science, 297, 1301-1310.
3. Bobek, L.A., Tsai, H., Biesbrock, A.R., and Levine, M.J. (1993) Molecular cloning, sequence, and specificity of expression of the gene encoding the low molecular weight human salivary mucin (MUC7). J. Biol. Chem., 268, 20563-20569.
4. Brenner, S., Elgar, G., Sandford, R., Macrae, A., Venkatesh, B., and Aparicio, S. (1993) Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature, 366, 265-268.
5. Davis, C.G., Elhammer, R.D.W., Schneider, W.J., Kornfeld, S., Brown, M.S., and Goldstein, J.L. (1986) Deletion of clustered O-linked carbohydrates does not impair function of low density lipoprotein receptor in transfected fibroblasts. J. Biol. Chem., 261, 2828-2838.
6. Desseyn, J.L., Buisine, M.P., Porchet, N., Aubert, J.P., and Laine, A. (1998) Genomic organization of the human mucin gene MUC5B-cDNA and genomic sequences upstream of the large central exon. J. Biol. Chem., 273, 30157-30164.
7. Desseyn, J.L., Aubert, J.P., Porchet, N., and Laine, A. (2000) Evolution of the large secreted gel-forming mucins. Mol. Biol. Evol., 17, 1175-1184.
8. Eckhardt, A.E., Timpte, C.S., DeLuca, A.W., and Hill, R.L. (1997) The complete cDNA sequence and structural polymorphism of the polypeptide chain of porcine submaxillary mucin. J. Biol. Chem., 272, 33204-33210.
9. Gendler, S.J. (2001) MUC1, the renaissance molecule. J. Mamm. Gland Biol. Neoplasia, 6, 339-353.
10. Gendler, S.J. and Spicer, A.P. (1995) Epithelial mucin genes. Ann. Rev. Physiol., 57, 607-634.
11. Gendler, S.J., Lancaster, C.A., Taylor-Papadimitriou, J., Duhig, T., Peat, N., Burchell, J., Pemberton, L., Lalani, E.N., and Wilson, D. (1990) Molecular cloning and expression of human tumor-associated polymorphic epithelial mucin. J. Biol. Chem., 265(25), 15286-15293.
12. Gum, J.R., Hicks, J.W., Toribara, N.W., Siddiki, B., and Kim, Y.S. (1994) Molecular cloning of human intestinal mucin (MUC2) cDNA. Identification of the amino terminus and overall sequence similarity to prepro-von Willebrand factor. J. Biol. Chem., 269, 2440-2446.
13. Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng., 10, 1-6.
14. Perez-Vilar, J. and Hill, R.L. (1999) The structure and assembly of secreted mucins. J. Biol. Chem., 274, 31751-31754.
15. Sadler, J.E. (1998) Biochemistry and genetics of von Willebrand factor. Ann. Rev. Biochem., 67, 395-424.
16. Sonnhammer, E.L., von Heijne, G., and Krogh, A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 175-182.
17. Spicer, A.P., Parry, G., Patton, S., and Gendler, S.J. (1991) Molecular cloning and analysis of the mouse homologue of the tumor-associated mucin, MUC1, reveals conservation of potential O-glycosylation sites, transmembrane, and cytoplasmic domains and a loss of minisatellite-like polymorphism. J. Biol. Chem., 266, 15099-15109.
18. Taupin, D. and Podolsky, D.K. (2003) Trefoil factors: Initiators of mucosal healing. Nat. Rev. Mol Cell Biol., 4, 721-723.
19. Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalities and weight matrix choice. Nucl. Acids Res., 22, 4673-4680.
20. Wreschner, D., McGuckin, M.A., Williams, S.J., Baruch, A., Yoell, M., Ziv, R., Okun, L., Zaretsky, J., Smorodinsky, N., Keydar, I., and others. (2002) Generation of ligand-receptor alliances by SEA module-mediated cleavage of membrane-associated mucin proteins. Protein Sci., 11, 698-706.
21. Yang, Z.Y., Duckers, H.J., Sullivan, N.J., Sanchez, A., Nabel, E.G., and Nabel, G.J. (2000) Identification of the Ebola virus glycoprotein as the main viral determinant of vascular cell cytotoxicity and injury. Nat. Med., 6, 886-889.