A global topology map of the Saccharomyces cerevisiae membrane proteome

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 30, 2006, Pages 11142-11147

  Kim, Hyun ^a   Melén, Karin ^a,b   Österberg, Marie ^a   Von Heijne, Gunnar ^a,b  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b ALBANOVA UNIVERSITY CENTER   (Sweden)

Author keywords

Membrane proteins; Membrane proteomics; Yeast

Indexed keywords

MEMBRANE PROTEIN; PROTEOME;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CELL MEMBRANE; EUKARYOTE; FUNGAL GENE; GENE SEQUENCE; GENOME; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

CELL MEMBRANE; COMPUTATIONAL BIOLOGY; FUNGAL PROTEINS; GENOME, FUNGAL; MEMBRANE PROTEINS; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 33746616385     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0604075103     Document Type: Article

References (57)

1. Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M., et al. (1996) Science 274, 562-567.
2. Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. & Barkai, N. (2002) Nat. Genet. 31, 370-377.
3. Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B., et al. (2002) Nature 418, 387-391.
4. Winzeler, E. A., Shoemaker, D. D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J. D., Bussey, H., et al. (1999) Science 285, 901-906.
5. Warringer, J., Ericson, E., Fernandez, L., Nerman, O. & Blomberg, A. (2003) Proc. Natl. Acad. Sci. USA 100, 15724-15729,
6. Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K. & Weissman, J. S. (2003) Nature 425, 737-741.
7. Sickmann, A., Reinders, J., Wagner, Y., Joppich, C., Zahedi, R., Meyer, H. E., Schonfisch, B., Perschil, I., Chacinska, A., Guiard, B., et al. (2003) Proc. Natl. Acad. Sci. USA 100, 13207-13212.
8. Kumar, A., Agarwal, S., Heyman, J. A., Matson, S., Heidtman, M., Piccirillo, S., Umansky, L., Drawid, A., Jansen, R., Liu, Y., et al. (2002) Genes Dev. 16, 707-719.
9. Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S. & O'Shea, E. K. (2003) Nature 425, 686-691.
10. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S. & Bork, P. (2002) Nature 417, 399-403.
11. Miller, J. P., Lo, R. S., Ben-Hur, A., Desmarais, C., Stagljar, I., Noble, W. S. & Fields, S. (2005) Proc. Natl. Acad. Sci. USA 102, 12123-12128.
12. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000) Nucleic Acids Res. 28, 235-242.
13. Jayasinghe, S., Hristova, K. & White, S. H. (2001) Protein Sci. 10, 455-458.
14. Melén, K., Krogh, A. & von Heijne, G. (2003) J. Mol. Biol. 327, 735-744.
15. Daley, D. O., Rapp, M., Granseth, E., Melén, K., Drew, D. & von Heijne, G. (2005) Science 308, 1321-1323.
16. Granseth, E., Daley, D. O., Rapp, M., Melén, K. & von Heijne, G. (2005) J. Mol. Biol. 352, 489-494.
17. Deak, R. & Wolf, D. (2001) J. Biol. Chem. 276, 10663-10669.
18. Kim, H., Melén, K. & von Heijne, G. (2003) J. Biol. Chem. 278, 10208-10213.
19. Gavin, A. C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Crucial, C. M., et al. (2002) Nature 415, 141-147.
20. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. (2001) J. Mol. Biol. 305, 567-580.
21. Riley, M. L., Schmidt, T., Wagner, C., Mewes, H. W. & Frishman, D. (2005) Nucleic Acids Res. 33, D308-D310.
22. Christie, K. R., Weng, S., Balakrishnan, R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J. E., et al. (2004) Nucleic Acids Res. 32, D311-D314.
23. Österberg, M., Kim, H., Warringer, J., Melén, K., Blomberg, A. & von Heijne, G. (2006) Proc. Natl. Acad. Sci. USA 103, 11148-11153.
24. van der Laan, M., Chacinska, A., Lind, M., Perschil, I., Sickmann, A., Meyer, H. E., Guiard, B., Meisinger, C., Pfanner, N. & Rehling, P. (2005) Mol. Cell. Biol. 25, 7449-7458.
25. Emanuelsson, O., Nielsen, H., Brunak, S. & von Heijne, G. (2000) J. Mol. Biol. 300, 1005-1016.
26. Kim, H., Yan, Q., von Heijne, G., Caputo, G. A. & Lennarz, W. J. (2003) Proc. Natl. Acad. Sci. USA 100, 7460-7464.
27. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990) J. Mol. Biol. 215, 403-410.
28. Palkova, Z., Devaux, F., Icicova, M., Minarikova, L., Le Crora, S. & Jacq, C. (2002) Mol. Biol. Cell 13, 3901-3914.
29. Spode, I., Maiwald, D., Hollenberg, C. P. & Suckow, M. (2002) J. Mol. Biol. 319, 407-420.
30. von Heijne, G. (1986) EMBO J. 5, 3021-3027.
31. Sääf, A., Johansson, M., Wallin, E. & von Heijne, G. (1999) Proc. Natl. Acad. Sci. USA 96, 8540-8544.
32. Rapp, M., Seppälä, S., Granseth, E. & von Heijne, G. (2006) Nat. Struct. Mol. Biol. 13, 112-116.
33. Viklund, H. & Elofsson, A. (2004) Protein Sci. 13, 1908-1917.
34. Wistrand, M., Käll, L. & Sonnhammer, E. L. (2006) Protein Sci. 15, 509-521.
35. Ashburner, M., Ball, C., Blake, J., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al (2000) Nat. Genet. 25, 25-29.
36. Tusnady, G. E. & Simon, I. (2001) Bioinformatics 17, 849-850.
37. Hubbard, T., Andrews, D., Caccamo, M., Cameron, G., Chen, Y., Clamp, M., Clarke, L., Coates, G., Cox, T., Cunningham, F., et al. (2005) Nucleic Acids Res. 33, D447-D453.
38. Gough, J., Karplus, K., Hughey, R. & Chothia, C. (2001) J. Mol. Biol. 313, 903-919.
39. Strahl-Bolsinger, S. & Scheinost, A. (1999) J. Biol. Chem. 274, 9068-9075.
40. Mewes, H. W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Munsterkotter, M., Rudd, S. & Weil, B. (2002) Nucleic Acids Res. 30, 31-34.
41. Zhao, R. & Reithmeier, R. A. (2001) Am. J. Physiol. Cell Physiol. 281, C33-C45.
42. Hitt, R. & Wolf, D. H. (2004) FEMS Yeast Res. 4, 721-729.
43. Urbanowski, J. L. & Piper, R. C. (1999) J. Biol. Chem. 274, 38061-38070.
44. Garnier, C., Blondel, M. O. & Haguenauer-Tsapis, R. (1996) Mol. Microbiol. 21, 1061-1073.
45. Gilstring, C. F. & Ljungdahl, P. O. (2000) J. Biol. Chem. 275, 31488-31495.
46. Bleve, G., Zacheo, G., Cappello, M. S., Dellaglio, F. & Grieco, F. (2005) Biochem. J. 390, 145-155.
47. Monk, B. C., Montesinos, C., Ferguson, C., Leonard, K. & Serrano, R. (1991) J. Biol. Chem. 266, 18097-18103.
48. Tcheperegine, S. E., Marelli, M. & Wozniak, R. W. (1999) J. Biol. Chem. 274, 5252-5258.
49. Konrad, G., Schlecker, T., Faulhammer, F. & Mayinger, P. (2002) J. Biol. Chem. 277, 10547-10554.
50. Wilkinson, B. M., Critchley, A. J. & Stirling, C. J. (1996) J. Biol. Chem. 271, 25590-25597.
51. Feldheim, D., Rothblatt, J. & Schekman, R. (1992) Mol. Cell. Biol. 12, 3288-3296.
52. Ljungdahl, P. O., Gimeno, C. J., Styles, C. A. & Fink, G. R. (1992) Cell 71, 463-478.
53. Romano, J. D. & Michaelis, S. (2001) Mol. Biol. Cell 12, 1957-1971.
54. Tam, A., Schmidt, W. K. & Michaelis, S. (2001) J. Biol. Chem. 276, 46798-46806.
55. Spirig, U., Glavas, M., Bodmer, D., Reiss, G., Burda, P., Lippuner, V., te Heesen, S. & Aebi, M. (1997) Mol. Gen. Genet. 256, 628-637.
56. Kim, H., von Heijne, G. & Nilsson, I. (2005) J. Biol. Chem. 280, 20261-20267.
57. Flannery, A. R., Graham, L. A. & Stevens, T. H. (2004) J. Biol. Chem. 279, 39856-39862.