Orphan Protein Function and Its Relation to Glycosylation
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Since the first bacterial genomes were completely sequenced, the surge in genome sequence data has overwhelmed the scientific community’s efforts towards elucidating protein function. Computational methods have made it possible to work with sequences from complete genomes and proteomes, and inference of protein function by exploiting direct sequence similarity indeed goes a long way in describing a proteome’s functional capacity. However, at least 40% of the gene products in newly sequenced genomes typically remain uncharacterised. Proteins without an annotated function are also known as orphan proteins since they do not belong to a functionally characterised protein family. Many sequences must, therefore, be compared using their features rather than by direct comparison in the conventional sequence space. Here we focus on one such feature — glycosylation — that is common in eukaryotic proteomes.
KeywordsGlycosylation Site Protein Chain Dictyostelium Discoideum Phylogenetic Profile Cellular Role
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- Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J, Davis A, Dolinski K, Dwight S, Eppig J, Harris M, Hill D, Issel Tarver L, Kasarskis A, Lewis S, Matese J, Richardson J, Ringwald M, Rubin G, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25–29Google Scholar
- Casari G, Ouzounis C, Valencia A, Sander C (1996) Genequiz-H: Automatic function assignment for genome sequence analysis. In: Hunter L, Klein T (eds) Proceedings of the First Annual Pacific Symposium on Biocomputing. World Scientific, Hawaii, pp 707–709Google Scholar
- Corner F, Hart G (2000) 0-Glycosylation of nuclear and cytosolic proteins: dynamic interplay between O-G1cNAc and O-Phosphate. J Biol Chem 275: 29179–29182Google Scholar
- Hart GW, Greis KD, Dong LY, Blomberg MA, Chou TY, Jiang MS, Roquemore EP, Snow DM, Kreppel LK, Cole RN (1995) 0-linked N-acetylglucosamine: the “yin-yang” of Ser/Thr phosphorylation? Nuclear and cytoplasmic glycosylation. Adv Exp Med Biol 376: 115–123Google Scholar
- Hounsell EF, Davies MJ, Renouf DV (1996) 0-linked protein glycosylation structure and function. Glycoconjugate J 13: 19–26Google Scholar
- Lis H, Sharon N (1993) Protein glycosylation: Structural and functional aspects. Cur J Biochem 218: 1–27Google Scholar
- 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 RGoogle Scholar
- Sankoff D, Sensen C (eds) Proceedings, Sixth International Conference on Intelligent Systems for Molecular Biology, vol. 6. AAAI Press, Menlo Park, pp 122–130Google Scholar
- Rubin G, Yandell M, Wortman J, Gabor Miklos G, Nelson C, Hariharan I, Fortini M, Li P, Apweiler R, Fleischmann W, Cherry J, Henikofi S, Skupski M, Misra S, Ashburner M, Birney E, Boguski M, Brody T, Brokstein P, Celniker S, Chervitz S, Coates D, Cravchik A, Gabrielian A, Galle R, Gelbart W, George R, Goldstein L, Gong F, Guan P, Harris N, Hay B, Hoskins R, Li J, Li Z, Hynes R, Jones S, Kuehl P, Lemaitre B, Littleton J, Morrison D, Mungall C, OFarrell P, Pickeral O, Shue C, Vosshall L, Zhang J, Zhao Q, Zheg X, Zhong F, Zhong W, Gibbs R, Venter J, Adams M, Lewis S (2000) Comparative genomics of the eukaryotes. Science 287: 2204–2215PubMedCrossRefGoogle Scholar