Revealing Static and Dynamic Modular Architecture of the Eukaryotic Protein Interaction Network

Overview

Journal Mol Syst Biol

Specialty Molecular Biology

Date 2007 Apr 25

PMID 17453049

Citations 48

Authors

Kakajan Komurov

Michael White

Affiliations

Soon will be listed here.

Abstract

In an effort to understand the dynamic organization of the protein interaction network and its role in the regulation of cell behavior, positioning of proteins into specific network localities was studied with respect to their expression dynamics. First, we find that constitutively expressed and dynamically co-regulated proteins cluster in distinct functionally specialized network neighborhoods to form static and dynamic functional modules, respectively. Then, we show that whereas dynamic modules are mainly responsible for condition-dependent regulation of cell behavior, static modules provide robustness to the cell against genetic perturbations or protein expression noise, and therefore may act as buffers of evolutionary as well as population variations in cell behavior. Observations in this study refine the previously proposed model of dynamic modularity in the protein interaction network, and propose a link between the evolution of gene expression regulation and biological robustness.

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References

Mewes H, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G . MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res. 2003; 32(Database issue):D41-4. PMC: 308826. DOI: 10.1093/nar/gkh092. View

Milo R, Itzkovitz S, Kashtan N, Chklovskii D, Alon U . Network motifs: simple building blocks of complex networks. Science. 2002; 298(5594):824-7. DOI: 10.1126/science.298.5594.824. View

Higashio H, Kohno K . A genetic link between the unfolded protein response and vesicle formation from the endoplasmic reticulum. Biochem Biophys Res Commun. 2002; 296(3):568-74. DOI: 10.1016/s0006-291x(02)00923-3. View

Ravasz E, Somera A, Mongru D, Oltvai Z, Barabasi A . Hierarchical organization of modularity in metabolic networks. Science. 2002; 297(5586):1551-5. DOI: 10.1126/science.1073374. View

Han J, Bertin N, Hao T, Goldberg D, Berriz G, Zhang L . Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature. 2004; 430(6995):88-93. DOI: 10.1038/nature02555. View

Papp B, Pal C, Hurst L . Dosage sensitivity and the evolution of gene families in yeast. Nature. 2003; 424(6945):194-7. DOI: 10.1038/nature01771. View

de la Fuente A, Bing N, Hoeschele I, Mendes P . Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics. 2004; 20(18):3565-74. DOI: 10.1093/bioinformatics/bth445. View

Krogan N, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A . Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006; 440(7084):637-43. DOI: 10.1038/nature04670. View

Segal E, Yelensky R, Koller D . Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics. 2003; 19 Suppl 1:i273-82. DOI: 10.1093/bioinformatics/btg1038. View

10.

Pal C, Papp B, Hurst L . Highly expressed genes in yeast evolve slowly. Genetics. 2001; 158(2):927-31. PMC: 1461684. DOI: 10.1093/genetics/158.2.927. View

11.

Newman J, Ghaemmaghami S, Ihmels J, Breslow D, Noble M, DeRisi J . Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature. 2006; 441(7095):840-6. DOI: 10.1038/nature04785. View

12.

Maslov S, Sneppen K . Specificity and stability in topology of protein networks. Science. 2002; 296(5569):910-3. DOI: 10.1126/science.1065103. View

13.

Lee D, Ezhkova E, Li B, Pattenden S, Tansey W, Workman J . The proteasome regulatory particle alters the SAGA coactivator to enhance its interactions with transcriptional activators. Cell. 2005; 123(3):423-36. DOI: 10.1016/j.cell.2005.08.015. View

14.

Luscombe N, Babu M, Yu H, Snyder M, Teichmann S, Gerstein M . Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 2004; 431(7006):308-12. DOI: 10.1038/nature02782. View

15.

Lee T, Linstedt A . Osmotically induced cell volume changes alter anterograde and retrograde transport, Golgi structure, and COPI dissociation. Mol Biol Cell. 1999; 10(5):1445-62. PMC: 25298. DOI: 10.1091/mbc.10.5.1445. View

16.

Gasch A, Spellman P, Kao C, Eisen M, Storz G, Botstein D . Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000; 11(12):4241-57. PMC: 15070. DOI: 10.1091/mbc.11.12.4241. View

17.

Harbison C, Gordon D, Lee T, Rinaldi N, MacIsaac K, Danford T . Transcriptional regulatory code of a eukaryotic genome. Nature. 2004; 431(7004):99-104. PMC: 3006441. DOI: 10.1038/nature02800. View

18.

Jeong H, Mason S, Barabasi A, Oltvai Z . Lethality and centrality in protein networks. Nature. 2001; 411(6833):41-2. DOI: 10.1038/35075138. View

19.

Ge H, Liu Z, Church G, Vidal M . Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet. 2001; 29(4):482-6. DOI: 10.1038/ng776. View

20.

Sato M, Sato K, Nakano A . Evidence for the intimate relationship between vesicle budding from the ER and the unfolded protein response. Biochem Biophys Res Commun. 2002; 296(3):560-7. DOI: 10.1016/s0006-291x(02)00922-1. View