Prediction of potential GPI-modification sites in proprotein sequences

Journal of Molecular Biology

Volumn 292, Issue 3, 1999, Pages 741-758

  Eisenhaber, Birgit ^a,b,c   Bork, Peer ^a,b   Eisenhaber, Frank ^a,b,c  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^c RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

Author keywords

Amino acid index; Genome annotation; GPI lipid anchor attachment; GPI modification prediction; Posttranslational modification

Indexed keywords

GLYCOSYLPHOSPHATIDYLINOSITOL; MUTANT PROTEIN; PROTEIN PRECURSOR;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPUTER PROGRAM; DATA BASE; INTERNET; METAZOON; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTOZOON;

EID: 0033600935     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3069     Document Type: Article

References (80)

1. Aceto J., Kieber-Emmons T., Cines D. B. Carboxy-terminal processing of the urokinase receptor: implications for substrate recognition and glycosylphosphatidylinositol anchor addition. Biochemistry. 38:1999;992-1001.
2. Altschul S., Boguski M., Gish W., Wootton J. C. Issues in searching molecular sequence databases. Nature Genet. 6:1994;119-129.
3. Antony A., Miller M. E. Statistical prediction of the locus of endoproteolytic cleavage of the nascent polypeptide in glycosylphosphatidylinositol-anchored proteins. Biochem. J. 298:1994;9-16.
4. Bairoch A., Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucl. Acids Res. 27:1999;49-54.
5. Beghdadi-Rais C., Schreyer M., Rousseaux M., Borel P., Eisenberg R. J., Cohen G. H., Bron C., Fasel N. Carboxyl terminus structural requirements for glycosyl-phosphatidylinositol anchor addition to cell surface proteins. J. Cell Sci. 105:1993;831-840.
6. Berger J., Howard A. D., Brink L., Gerber L. D., Hauber J., Cullen B. R., Udenfriend S. COOH-terminal requirements for the correct processing of a phosphatidylinositol-glycan anchored membrane protein. J. Biol. Chem. 263:1988;10016-10021.
7. Birney E., Thompson J. D., Gibson T. J. PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucl. Acid Res. 24:1996;2730-2739.
8. Bork P., Gibson T. J. Applying motif and profile searches. Methods Enzymol. 266:1996;162-184.
9. Bork P., Dandekar T., Diaz-Lazcoz Y., Eisenhaber F., Huynen M., Yuan Y. Predicting function: from genes to genomes and back. J. Mol. Biol. 283:1998;707-725.
10. Brennan P. J., Nikaido H. The envelope of mycobacteria. Annu. Rev. Biochem. 64:1995;29-63.
11. Bucht G., Hjalmarsson K. Residues in Torpedo californica acetylcholinesterase necessary for processing to a glycosyl phophatidylinositol-anchored form. Biochim. Biophys. Acta. 1292:1996;223-232.
12. Bucht G., Wikström P., Hjalmarsson K. Optimising the signal peptide for GPI modification of human acetylcholinesterase using mutational analysis and peptide-QSAR. Biochim. Biophys. Acta. 1431:1999;471-482.
13. Caras I. W. An internally positioned signal can direct attachment of a glycophospholipid membrane anchor. J. Cell Biol. 113:1991;77-85.
14. Caras I. W., Weddel G. N. Signal peptide for protein secretion directing glycophospholipid membrane anchor attachment. Science. 243:1989;1196-1198.
15. Caras I. W., Weddel G. N., Williams S. R. Analysis of the signal for attachment of a glycophospholipid membrane anchor. J. Cell Biol. 108:1989;1387-1396.
16. Chen R., Walter E. I., Parker G., Lapurga J. P., Millan J. L., Ikehara Y., Udenfriend S., Medof M. E. Mammalian glycophosphatidylinositol anchor transfer to proteins and posttransfer deacylation. Proc. Natl Acad. Sci. USA. 95:1998;9512-9517.
17. Chou K.-C., Elrod D. W. Prediction of membrane protein types and subcellular locations. Proteins: Struct. Funct. Genet. 34:1999;137-153.
18. Clayton C. E., Mowatt M. R. The procyclic acididc repetitive proteins of Trypanosoma brucei. J. Biol. Chem. 264:1989;15088-15093.
19. Coyne K. E., Crisci A., Lublin D. M. Construction of synthetic signals for glycosyl-phosphatidylinositol anchor attachment. J. Biol. Chem. 268:1993;6689-6693.
20. Eisenhaber F., Bork P. Wanted: subcellular localization of proteins based on sequence. Trends Cell Biol. 8:1998a;169-170.
21. Eisenhaber F., Bork P. Sequence and structure of proteins. Mountain A., Ney U., Schomburg D. Biotechnology Recombinant Proteins, Monoclonal Antibodies and Therapeutic Genes. 1998b;47-86 VCH-Wiley, Weinheim.
22. Eisenhaber F., Bork P. Computer-evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries. Bioinformatics. 15:1999;in the press.
23. Eisenhaber B., Bork P., Eisenhaber F. Sequence properties of GPI-anchored proteins near the ω-site: constraints for the polypeptide binding site of the putative transamidase. Protein Eng. 11:1998;1155-1161.
24. Engle M. J., Mahmood A., Alpers D. H. Two rat intestinal alkaline phosphatase isoforms with different carboxyl-terminal peptides are both membrane-bound by a glycan phosphatidylinositol linkage. J. Biol. Chem. 270:1995;11935-11940.
25. Ferguson M. A., Williams A. F. Cell-surface anchoring of proteins via glycosyl-phosphatidylinositol structures. Annu. Rev. Biochem. 57:1988;285-320.
26. Furukawa Y., Tamura H., Ikezawa H. Mutational analysis of the COOH-terminal hydrophobic domain of bovine liver 5′-nucleotidase as a signal for glycosylphosphatidylinositol (GPI) anchor attachment. Biochim. Biophys. Acta. 1190:1994;273-278.
27. Furukawa Y., Tsukamoto K., Ikezawa H. Mutational analysis of the C-terminal signal peptide of bovine liver 5′-nucleotidase for GPI anchoring: a study on the significance of the hydrophilic spacer region. Biochim. Biophys. Acta. 1328:1997;185-196.
28. Gerber L. D., Kodukula K., Udenfriend S. Phosphatidylinositol glycan (PI-G) anchored membrane proteins. J. Biol. Chem. 267:1992;12168-12173.
29. Guadiz G., Haidaris C. G., Maine G. N., Simpson-Haidaris P. J. The carboxyl terminus of Pneumocystis carinii glycoprotein A encodes a functional glycosylphosphatidylinositol signal sequence. J. Biol. Chem. 273:1998;26202-26209.
30. Harpaz Y., Gerstein M., Chothia C. Volume changes on protein folding. Structure. 2:1994;641-649.
31. Heringa J., Sommerfeldt H., Higgins D., Argos P. OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. Comput. Appl. Biosci. 8:1992;599-600.
32. Hettmann T., Schmidt C. L., Anemüller S., Zähringer U., Moll H., Petersen A., Schäfer G. Cytochrome b558/566 from the archaeon Sulfolobus acidocaldarius. J. Biol. Chem. 273:1998;12032-12040.
33. Hobohm U., Scharf M., Schneider R., Sander C. Selection of representative protein data sets. Protein Sci. 1:1992;409-417.
34. Howell S., Lanctôt C., Boileau G., Crine P. A cleavable N-terminal signal peptide is not a prerequisite for the biosynthesis of glycosylphosphatidylinositol-anchored proteins. J. Biol. Chem. 269:1994;16993-16996.
35. Ilangumaran S., Robinson P. J. Transfer of exogeneous glycosylphosphatidylinositol (GPI)-linked molekules to plasma membranes. Trends Cell Biol. 6:1996;163-167.
36. Ilangumaran S., Arni S., Poincelet M., Theler J.-M., Brennan P. J., ud-Din N., Hoessli D. C. Integration of mycobacterial lipoarabinomannans into glycosylphosphatidylinositol-rich domains of lymphomonocytic cell plasma membranes. J. Immunol. 155:1995;1334-1342.
37. Killeen N., Moessner R., Arvieux J., Willis A., Williams A. F. The MRC OX-45 antigen of rat leukocytes and endothelium is in a subset of the immunoglobulin superfamily with CD2, LF-3 and carcinoembryonic antigens. EMBO J. 7:1988;3087-3091.
38. Kobayashi T., Nishizaki R., Ikezawa H. The presence of GPI-linked protein(s) in an archaeobacterium, Sulfolobus acidocaldarius, closely related to eukaryotes. Biochim. Biophys. Acta. 1334:1997;1-4.
39. Kodukula K., Gerber L. D., Amthauer R., Brink L., Udenfriend S. Biosynthesis of glycosylphosphatidylinositol (GPI)-anchored membrane proteins in intact cells: specific amino acid requirements adjacent to the site of cleavage and GPI attachment. J. Cell Biol. 120:1993;657-664.
40. Kurosaki T., Ravetch J. V. A single amino acid in the glycosyl phosphatidylinositol attachment domain determines the membrane topology of FcγRIII. Nature. 342:1989;805-807.
41. Low M. G., Stiernberg J., Waneck G. L., Flavell R. A., Kincade P. W. Cell-specific heterogeneity in sensitivity of phosphatidylinositol-anchored membrane antigens to release by phospholipase C. J. Immunol. Methods. 113:1988;101-111.
42. Lowe M. E. Site-specific mutations in the COOH-terminus of placental alkaline phosphatase: a single amino acid change converts a glycosylphosphatidylinositol-glycan-anchored protein to a secreted protein. J. Cell Biol. 116:1992;799-807.
43. Micanovic R., Gerber L. D., Berger J., Kodukula K., Udenfriend S. Selectivity of the cleavage/attachment site of phosphatidylinositol-glycan-anchored membrane proteins determined by site-specific mutagenesis at Asp-484 of placental alkaline phosphatase. Proc. Natl Acad. Sci. USA. 87:1990;157-161.
44. Misumi Y., Ogata S., Ohkubo K., Hirose S., Ikehara Y. Primary structure of human placental 5′-nucleotidase and identification of the glycolipid anchor in the mature form. FEBS Letters. 191:1990;563-569.
45. Moran P., Caras I. W. Fusion of sequence elements from non-anchored proteins to generate a fully functional signal for glycosylphosphatidylinositol membrane anchor attachment. J. Cell. Biol. 115:1991;1595-1600.
46. Moran P., Caras I. W. Requirements for glycosylphosphatidylinositol attachment are similar but not identical in mammalian cells and parasitic Protozoa. J. Cell. Biol. 125:1994;333-343.
47. Moran P., Raab H., Kohr W. J., Caras I. W. Glycophospholipid membrane anchor attachment. J. Biol. Chem. 266:1991;1250-1257.
48. Morita N., Nakazato H., Okuyama H., Kim Y., Thompson G. A. Jr. Evidence for a glycosylinositolphospholipid-anchored alkaline phophatase in the aquatic plant Spirodela oligorrhiza. Biochim. Biophys. Acta. 1290:1996;53-62.
49. Nakai K., Horton P. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24:1999;34-35.
50. Nakai K., Kanehisa M. A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics. 14:1997;897-911.
51. Nakashima H., Nishikawa K. The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins. FEBS Letters. 303:1992;141-146.
52. Nielsen H., Brunak S., von Heijne G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng. 12:1999;3-9.
53. Nosjean O., Briolay A., Roux B. Mammalian GPI proteins: sorting, membrane residence and functions. Biochim. Biophys. Acta. 1331:1997;153-186.
54. Nuoffer C., Jenö P., Conzelmann A., Riezmann H. Determinants for glycophospholipid anchoring of the Saccharomyces cerevisae GAS1 protein to the plasma membrane. Mol. Cell. Biol. 11:1991;27-37.
55. Nuoffer C., Horvath A., Riezmann H. Analysis of the sequence requirements for glycosylphosphatidylinositol anchoring of Saccharomyces cerevisiae Gas1 protein. J. Biol. Chem. 268:1993;10558-10563.
56. Ogata S., Hayashi Y., Misumi Y., Ikehara Y. Membrane-anchoring domain of rat liver 5′-nucleotidase: identification of the COOH-terminal serine-523 covalently attached with a glycolipid. Biochemistry. 29:1990;7923-7927.
57. Okuyama T., Waheed A., Kusumoto W., Zhu X. L., Sly W. S. Carbonic anhydrase IV: role of removal of C-terminal domain in glycosylphosphatidylinositol anchoring and realization of enzyme activity. Arch. Biochem. Biophys. 320:1995;315-322.
58. Orchansky P. L., Escobedo J. A., Williams L. T. Phosphatidylinositol linkage of a truncated form of the platelet-derived growth factor receptor. J. Biol. Chem. 263:1988;15159-15165.
59. Santillán G. E., Sandoval M. J., Chernajovsky Y., Orchansky P. L. Conversion of human interferon-β from a secreted to a phosphatidylinositol anchored protein by fusion of a 17 amino acid sequence to its carboxyl terminus. Mol. Cell. Biochem. 110:1992;181-191.
60. Shen F., Wu M., Ross J. F., Miller D., Ratnam M. Folate receptor type γ is primarily a secretory protein due to lack of an efficient signal for glycosylphosphatidylinositol modification: protein characterization and cell type specifity. Biochemistry. 34:1995;5660-5665.
61. Stahl N., Baldwin M. A., Burlingame A. L., Prusiner S. B. Identification of glycoinositol phospholipid linked and truncated forms of the scrapie prion protein. Biochemistry. 29:1990;8879-8884.
62. Su B., Bothwell A. L. M. Biosynthesis of a glycosylphosphatidylinositol-glycan-linked membrane protein:signals for posttranslational processing of the Ly-6E antigen. Mol. Cell. Biol. 9:1989;3369-3376.
63. Sugita Y., Nakano Y., Oda E., Noda K., Tobe T., Miura N. H., Tomita M. Determination of carboxy-terminal residue and disulphide bonds of MACIF (CD59), a glycosyl-phosphatidylinositol-anchored membrane protein. J. Biochem. 114:1993;473-477.
64. Sunyaev S. R., Eisenhaber F., Rodchenkov I. V., Eisenhaber B., Tumanyan V. G., Kuznetsov E. N. PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng. 12:1999;387-394.
65. Suzuki K., Furukawa Y., Tamura H., Ejiri N., Suematsu H., Taguchi R., Nakamura S., Suzuki Y., Ikezawa H. Purification and cDNA cloning of bovine liver 5′-Nucleotidase, a GPI-anchored protein, and its expression in COS cells. J. Biochem. 113:1993;607-613.
66. Taguchi R., Hamakawa N., Harada-Nishida M., Fukui T., Nojima K., Ikezawa H. Microheterogeneity in glycosylphosphatidylinositol anchor structures of bovine liver 5′-nucleotidase. Biochemistry. 33:1994;1017-1022.
67. Taguchi R., Yamazaki J., Takahashi K., Hirano A., Ikezawa H. Identification of a new glycosylphosphatidylinositol-anchored 42-kDa protein and its C-terminal peptides from bovine erythrocytes by gas chromatography-, time-of-flight-, and electrospray-ionization-mass spectrometry. Arch. Biochem. Biophys. 363:1999;60-67.
68. Takos A. M., Dry I. B., Soole K. L. Detection of glycosyl-phosphatidylinositol-anchored proteins on the surface of Nicotiana tabacum protoplasts. FEBS Letters. 405:1997;1-4.
69. Tomassetti A., Bottero F., Mazzi M., Miotti S., Colnaghi M. I., Canevari S. Molecular requirements for attachment of the glycosylphosphatidylinositol anchor to the human alpha folate receptor. J. Cell Biol. 72:1999;111-118.
70. Tse A. G. D., Barclay A. N., Watts A., Williams A. F. A glycophospholipid tail at the carboxyl terminus of the Thy-1 glycoprotein of neurons and thymocytes. Science. 230:1985;1003-1008.
71. Udenfriend S., Kodukula K. How glycosylphosphatidylinositol-anchored membrane proteins are made. Annu. Rev. Biochem. 64:1995a;563-591.
72. Udenfriend S., Kodukula K. Prediction of omega site in nascent precursor of glycosylphosphatidylinositol protein. Methods Enzymol. 250:1995b;571-582.
73. Vai M., Lacanà E., Gatti E., Breviario D., Popolo L., Alberghina L. Evolutionary conservation of genomic sequences related to the GGP1 gene encoding a yeast GPI-anchored glycoprotein. Curr. Genet. 23:1993;19-21.
74. Waneck G. L., Stein M. E., Flavell R. A. Conversion of a PI-anchored protein to an integral membrane protein by a single amino acid mutation. Science. 241:1988;697-699.
75. Wang J., Shen F., Yan W., Wu M., Ratnam M. Proteolysis of the carboxyl-terminal GPI signal independent of GPI modification as a mechanism for selective protein secretion. Biochemistry. 36:1997;14583-14592.
76. Wang J., Maziarz K., Ratnam M. Recognition of the carboxyl-terminal signal for GPI modification requires translocation of its hydrophobic domain across the ER membrane. J. Mol. Biol. 286:1999;1303-1310.
77. Wilbourn B., Nesbeth D., Wainwright L. J., Field M. C. Proteasome and thiol involvement in quality control of glycosylphosphatidylinositol anchor addition. Biochem. J. 332:1998;111-118.
78. Yan W., Ratnam M. Preferred sites of glycosylphosphatidylinositol modification in folate receptors and constraints in the primary structure of the hydrophobic portion of the signal. Biochemistry. 34:1995;14594-14600.
79. Yan W., Shen F., Dillon B., Ratnam M. The hydrophobic domains in the carboxyl-terminal signal for GPI modification and in the amino-terminal leader peptide have similar structural requirements. J. Mol. Biol. 275:1998;25-33.
80. Zhou J., Dutch R. E., Lamb R. A. Proper Spacing between Heptad repeat B and the transmembrane domain boundary of the paramyxovirus SV5 F protein is critical for biological activity. Virology. 239:1997;327-339.