Cohesive versus flexible evolution of functional modules in eukaryotes

PLoS Computational Biology

Volumn 5, Issue 1, 2009, Pages

  Fokkens, Like ^a,b   Snel, Berend ^a,b  

^a UTRECHT UNIVERSITY   (Netherlands)

^b UTRECHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY;

BIOCHEMICAL PATHWAY; CASE STUDY ANALYSIS; CEREVISIAE; EUKARYOTIC GENOME; FUNCTIONAL MODULES; PHYLOGENETIC PROFILE; PROTEIN COMPLEXES; PROTEIN PATHWAYS; SYSTEMATIC ANALYSIS;

PROTEINS;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; EUKARYOTE; GENOME; MOLECULAR EVOLUTION; SACCHAROMYCES CEREVISIAE; BIOLOGICAL MODEL; BIOLOGY; EUKARYOTIC CELL; METABOLISM; METHODOLOGY; PHYLOGENY; PHYSIOLOGY; PROTEIN DATABASE;

EUKARYOTA; PROKARYOTA;

PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; METABOLIC NETWORKS AND PATHWAYS; MODELS, GENETIC; PHYLOGENY; PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 59149100474     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000276     Document Type: Article

References (30)

1. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A 96: 4285-4288.
2. Monahan BJ, Villen J, Marguerat S, Bahler J, Gygi SP, et al. (2008) Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast. Nat Struct Mol Biol 15: 873-880.
3. Huynen MA, Dandekar T, Bork P (1999) Variation and evolution of the citric-acid cycle: a genomic perspective. Trends Microbiol 7: 281-291.
4. Gabaldon T, Rainey D, Huynen MA (2005) Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (complex I). J Mol Biol 348: 857-870.
5. Tanaka T, Tateno Y, Gojobori T (2005) Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes. Mol Biol Evol 22: 243-250.
6. Smits P, Smeitink JA, van den Heuvel LP, Huynen MA, Ettema TJ (2007) Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Res 35: 4686-4703.
7. Singh AH, Wolf DM, Wang P, Arkin AP (2008) Modularity of stress response evolution. Proc Natl Acad Sci U S A 105: 7500-7505.
8. Bourbon HM (2008) Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex. Nucleic Acids Res 36: 3993-4008.
9. Snel B, Huynen MA (2004) Quantifying modularity in the evolution of biomolecular systems. Genome Res 14: 391-397.
10. Glazko GV, Mushegian AR (2004) Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns. Genome Biol 5: R32.
11. Campillos M, von Mering C, Jensen LJ, Bork P (2006) Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Res 16: 374-382.
12. Snitkin ESGA, Mellor J, Wu J, DeLisi C (2006) Comparative assessment of performance and genome dependence among phylogenetic profiling methods. BMC Bioinformatics 7: 420.
13. Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41.
14. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
15. Collins S, Kemmeren P, Zhao X-C, Greenblatt J, Spencer F, et al. (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 6: 439-450.
16. Li L, Stoeckert JCJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
17. Hirsh A, Fraser H, Wall D (2005) Adjusting for selection on synonymous sites in estimates of evolutionary distance. Mol Biol Evol 22: 174-177.
18. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
19. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
20. Pazos F, Valencia A (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng 14: 609-614.
21. Neher E (1994) How frequent are correlated changes in families of protein sequences? Proc Natl Acad Sci U S A 91: 98-102.
22. Cordero OX, Snel B, Hogeweg P (2008) Coevolution of gene families in prokaryotes. Genome Res 18: 462-468.
23. Jothi R, Przytycka TM, Aravind L (2007) Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics 8: 173.
24. Kroiss M, Schultz J, Wiesner J, Chari A, Sickmann A, et al. (2008) Evolution of an RNP assembly system: a minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster. Proc Natl Acad Sci U S A 105: 10045-10050.
25. Mewes HW, Dietmann S, Frishman D, Gregory R, Mannhaupt G, et al. (2008) MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Res 36: D196-D201.
26. Aloy P, Bottcher B, Ceulemans H, Leutwein C, Mellwig C, et al. (2004) Structure-based assembly of protein complexes in yeast. Science 303: 2026-2029.
27. Rognes T (2001) ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches. Nucleic Acids Res 29: 1647-1652.
28. Remm M, Storm CE, Sonnhammer EL (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-1052.
29. Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T (2006) CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22: 1021-1023.
30. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.