Protein feature based identification of cell cycle regulated proteins in yeast

Journal of Molecular Biology

Volumn 329, Issue 4, 2003, Pages 663-674

  De Lichtenberg, Ulrik ^a   Jensen, Thomas S ^a   Jensen, Lars J ^a   Brunak, Søren ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

Cell cycle; Instability degradation; Phosphorylation; Proteome dynamics; Subcellular location

Indexed keywords

CELL CYCLE PROTEIN; PROTEOME; REGULATOR PROTEIN;

ARTICLE; CELL CYCLE; CELLULAR DISTRIBUTION; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENETIC CODE; GLYCOSYLATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; PROTEIN STABILITY; REGULATOR GENE; YEAST;

EID: 0038412810     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00490-X     Document Type: Article

References (33)

1. Mendenhall M., Hodge A. Regulation of Cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 62:1998;1191-1243.
2. Breeden L. Cyclin transcription: timing is everything. Curr. Biol. 10:2000;R586-R588.
3. Tyers M., Jorgensen P. Proteolysis and the cell cycle: with this RING I do thee destroy. Curr. Opin. Genet. Dev. 10:2000;54-64.
4. Nurse P. A long twentieth century of the cell cycle and beyond. Cell. 100:2000;71-78.
5. Cho R., Campbell M., Winzeler E., Steinmetz L., Conway A., Wodicka L., et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell. 2:1998;65-73.
6. Spellman P., Sherlock G., Zhang M., Iyer V., Anders K., Eisen M., et al. Comprehensive identification of cell cycle-regulated genes of the yeast S. cerevisiae by microarray hybridization. Mol. Biol. Cell. 9:1998;3273-3297.
7. Zhao L., Prentice R., Breeden L. Statistical modeling of large microarray data sets to identify stimulus-response profiles. Proc. Natl Acad. Sci. USA. 98:2001;5631-5636.
8. Shedden K., Cooper S. Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods. Nucl. Acids Res. 30:2002;2920-2929.
9. Simon I., Barnett J., Hannett N., Harbison C., Ranaldi N., Volkert T., et al. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell. 106:2001;697-708.
10. Jensen L., Gupta R., Blom N., Devos D., Tamames J., Kesmir C., et al. Prediction of human protein function from post-translational modifications and localization features. J. Mol. Biol. 319:2002;1257-1265.
11. Goffeau A., Aert R., Agostini-Carbone M.L., Ahmed A., Aigle M., Alberghina L., et al. The yeast genome directory. Nature. 387:1997;5-105.
12. Wood V., Rutherford K., Ivens A., Rajandream M., Barrell B. A re-annotation of the Saccharomyces cerevisiae genome. Comp. Funct. Genom. 2:2001;143-154.
13. Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA. 98:2001;4569-4574.
14. Luca F., Mody M., Kurischko C., Roof D., Giddings T., Winey M. Saccharomyces cerevisiae mob1p is required for cytokinesis and mitotic exit. Mol. Cell. Biol. 21:2001;6972-6983.
15. Blom N., Gammeltoft S., Brunak S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol. 294:1999;1351-1362.
16. Rechsteiner M., Rogers S. PEST sequences and regulation by proteolysis. Trends Biochem. Sci. 21:1996;267-271.
17. Durocher D., Jackson S. The FHA domain. FEBS Letters. 513:2002;58-66.
18. Letunic I., Goodstadt L., Dickens N., Doerks T., Schultz J., Mott R., et al. Recent improvements to the SMART domain-based sequence annotation resource. Nucl. Acids Res. 30:2002;242-244.
19. Guruprasad K., Reddy B., Pandit M. Correlation between stability of a protein and its di-peptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng. 4:1990;155-161.
20. Lew D., Weinert T., Pringle J. Cell cycle control in Saccharomyces cerevisiae. Pringle J., Broach J., Jones E. The Molecular Biology of the Yeast Saccharomyces-3: Cell Cycle and Cell Biology. 1997;607-695 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
21. Murakami H., Nurse P. DNA replication and damage checkpoints and meiotic cell cycle controls in the fission and budding yeasts. Biochem. J. 349:2000;1-12.
22. Madeo F., Schlauer J., Zischka H., Mecke D., Frhlich K. Tyrosine phosphorylation regulates cell cycle dependent nuclear localization of cdc48p. Mol. Biol. Cell. 9:1998;131-141.
23. Hubbard T., Barker D., Birney E., Cameron G., Chen Y., Clark L., et al. The Ensembl genome database. Nucl. Acids Res. 30:2002;38-41.
24. Mathews B. Comparison of the predicted and observed secondary structure of t4 phage lysozyme. Biochim. Biophys. Acta. 405:1975;442-451.
25. Nakai K., Horton P. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24:1999;34-36.
26. Hansen J., Lund O., Tolstrup N., Gooley A., Williams K., Brunak S. NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycoconj. J. 15:1998;115-130.
27. Nielsen H., Brunak S., Engelbrecht J., von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1997;1-6.
28. Krogh A., Larsson B., von Heijne G., Sonnhammer E. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:2001;567-580.
29. Kyte J., Doolittle R. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:1982;105-132.
30. Lee T., Rinaldi N., Robert F., Odom D., Bar-Joseph Z., Gerber G., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 298:2002;799-804.
31. Iyer V., Horak C., Scafe C., Botstein D., Snyder M., Brown P. Genomics binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 409:2001;533-538.
32. Stevenson L., Kennedy B., Harlow E. A large-scale overexpression screen in Saccharomyces cerevisiae identifies previously uncharacterized cell cycle genes. Proc. Natl Acad. Sci. USA. 98:2001;3946-3951.
33. King, R. D., Karwath, A., Clare, A. & Dehapse, L. (2000). Accurate prediction of protein functional class in the M. tuberculosis and E. coli genomes using data mining. Yeast 17 (Comp. Funct. Genom. 1), 283-293.