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Dynamic Complex Formation During the Yeast Cell Cycle
Ulrik de Lichtenberg,1*Lars Juhl Jensen,2*Søren Brunak,1Peer Bork2,3
To analyze the dynamics of protein complexes during the yeastcell cycle, we integrated data on protein interactions and geneexpression. The resulting time-dependent interaction networkplaces both periodically and constitutively expressed proteinsin a temporal cell cycle context, thereby revealing previouslyunknown components and modules. We discovered that most complexesconsist of both periodically and constitutively expressed subunits,which suggests that the former control complex activity by amechanism of just-in-time assembly. Consistent with this, weshow that additional regulation through targeted degradationand phosphorylation by Cdc28p (Cdk1) specifically affects theperiodically expressed proteins.
1 Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark. 2 European Molecular Biology Laboratory, D-69117 Heidelberg, Germany. 3 Max-Delbrück-Centre for Molecular Medicine, D-13092 Berlin, Germany.
* These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail: bork{at}embl.de
The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast.
G. Musso, M. Costanzo, M. Huangfu, A. M. Smith, J. Paw, B.-J. San Luis, C. Boone, G. Giaever, C. Nislow, A. Emili, et al. (2008)
Genome Res.
18, 1092-1099
|Abstract »|Full Text »|PDF »
Plk1- and {beta}-TrCP-dependent degradation of Bora controls mitotic progression.
A. Seki, J. A. Coppinger, H. Du, C.-Y. Jang, J. R. Yates III, and G. Fang (2008)
J. Cell Biol.
181, 65-78
|Abstract »|Full Text »|PDF »
Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein-protein interaction dataset.
J. Guo, X. Wu, D.-Y. Zhang, and K. Lin (2008)
Nucleic Acids Res.
36, 2002-2011
|Abstract »|Full Text »|PDF »
High-resolution timing of cell cycle-regulated gene expression.
M. Rowicka, A. Kudlicki, B. P. Tu, and Z. Otwinowski (2007)
PNAS
104, 16892-16897
|Abstract »|Full Text »|PDF »
LICORN: learning cooperative regulation networks from gene expression data.
M. Elati, P. Neuvial, M. Bolotin-Fukuhara, E. Barillot, F. Radvanyi, and C. Rouveirol (2007)
Bioinformatics
23, 2407-2414
|Abstract »|Full Text »|PDF »
A bacterial two-hybrid system based on the twin-arginine transporter pathway of E. coli.
Thematic review series: Systems Biology Approaches to Metabolic and Cardiovascular Disorders. Multi-organ whole-genome measurements and reverse engineering to uncover gene networks underlying complex traits.
J. Tegner, J. Skogsberg, and J. Bjorkegren (2007)
J. Lipid Res.
48, 267-277
|Abstract »|Full Text »|PDF »
Transcriptional regulation of protein complexes within and across species.
K. Tan, T. Shlomi, H. Feizi, T. Ideker, and R. Sharan (2007)
PNAS
104, 1283-1288
|Abstract »|Full Text »|PDF »
CellCircuits: a database of protein network models.
H. C. Mak, M. Daly, B. Gruebel, and T. Ideker (2007)
Nucleic Acids Res.
35, D538-D545
|Abstract »|Full Text »|PDF »
Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights.
P. M. Kim, L. J. Lu, Y. Xia, and M. B. Gerstein (2006)
Science
314, 1938-1941
|Abstract »|Full Text »|PDF »
A Complex Oscillating Network of Signaling Genes Underlies the Mouse Segmentation Clock.
M.-L. Dequeant, E. Glynn, K. Gaudenz, M. Wahl, J. Chen, A. Mushegian, and O. Pourquie (2006)
Science
314, 1595-1598
|Abstract »|Full Text »|PDF »
A Network-based Analysis of Polyanion-binding Proteins Utilizing Yeast Protein Arrays.
N. Salamat-Miller, J. Fang, C. W. Seidel, A. M. Smalter, Y. Assenov, M. Albrecht, and C. R. Middaugh (2006)
Mol. Cell. Proteomics
5, 2263-2278
|Abstract »|Full Text »|PDF »
Genome-wide functional analysis of human cell-cycle regulators.
M. Mukherji, R. Bell, L. Supekova, Y. Wang, A. P. Orth, S. Batalov, L. Miraglia, D. Huesken, J. Lange, C. Martin, et al. (2006)
PNAS
103, 14819-14824
|Abstract »|Full Text »|PDF »
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T. Pramila, W. Wu, S. Miles, W. S. Noble, and L. L. Breeden (2006)
Genes & Dev.
20, 2266-2278
|Abstract »|Full Text »|PDF »
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E. P. Romijn, C. Christis, M. Wieffer, J. W. Gouw, A. Fullaondo, P. van der Sluijs, I. Braakman, and A. J. R. Heck (2005)
Mol. Cell. Proteomics
4, 1297-1310
|Abstract »|Full Text »|PDF »
Metabolic Engineering in the -omics Era: Elucidating and Modulating Regulatory Networks.
G. N. Vemuri and A. A. Aristidou (2005)
Microbiol. Mol. Biol. Rev.
69, 197-216
|Abstract »|Full Text »|PDF »
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