Evolution and topology in the yeast protein interaction network

Genome Research
Stefan Wuchty

Abstract

The integrity of the yeast protein-protein interaction network is maintained by a few highly connected proteins, or hubs, which hold the numerous less-connected proteins together. The structural importance and the increased essentiality of these proteins suggest that they are likely to be conserved in evolution, implying a strong relationship between the number of interactions and their evolutionary distance to its orthologs in other organisms. The existence of this coherence was recently reported to strongly depend on the quality of the protein interaction and orthologs data. Here, we introduce a novel method, the evolutionary excess retention (ER), allowing us to uncover a robust and strong correlation between the conservation, essentiality, and connectivity of a yeast protein. We conclude that the relevance of the hubs for the network integrity is simultaneously reflected by a considerable probability of simultaneously being evolutionarily conserved and essential, an observation that does not have an equivalent for nonessential proteins. Providing a thorough assessment of the impact noisy and incomplete data have on our findings, we conclude that our results are largely insensitive to the quality of the utilized data.

References

Oct 8, 1997·Journal of Molecular Evolution·N V Grishin
Jul 27, 1999·Current Biology : CB·L D Hurst, N G Smith
Aug 10, 2000·Nature·R AlbertA L Barabasi
Apr 3, 2001·Proceedings of the National Academy of Sciences of the United States of America·T ItoY Sakaki
Apr 11, 2001·Proceedings of the National Academy of Sciences of the United States of America·T R Hazbun, S Fields
May 3, 2001·Nature·H JeongZ N Oltvai
Jul 10, 2001·Journal of Molecular Evolution·L B Koski, G B Golding
Dec 18, 2001·Journal of Molecular Biology·M RemmE L Sonnhammer
Apr 27, 2002·Science·Hunter B FraserMarcus W Feldman
Dec 7, 2002·Proteomics·Stefan Wuchty
Apr 5, 2003·Proceedings of the National Academy of Sciences of the United States of America·Debra S Goldberg, Frederick P Roth
May 29, 2003·BMC Evolutionary Biology·Hunter B FraserAaron E Hirsh
Dec 14, 2004·Bioinformatics·D P WallA E Hirsh

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Citations

Apr 1, 2006·Planta·Joachim F Uhrig
May 4, 2010·Annals of Biomedical Engineering·Engin CukurogluOzlem Keskin
Mar 8, 2005·Drug Discovery Today·Martin G Grigorov
Oct 24, 2009·Nature Reviews. Molecular Cell Biology·Takuji Yamada, Peer Bork
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mehmet KoyutürkAnanth Grama
Jul 18, 2006·Bioinformatics·Pall F Jonsson, Paul A Bates
Mar 4, 2011·Bioinformatics·Andrew D FoxDonna K Slonim
Oct 30, 2010·Integrative and Comparative Biology·Quinlyn A SoltowDaniel E L Promislow
Jun 30, 2012·Nucleic Acids Research·Stefan WuchtyPeter O Bauer
Aug 10, 2005·Proceedings. Biological Sciences·Stéphane CoulombMarie-Claude Marsolier-Kergoat
Jul 5, 2006·Journal of Bioinformatics and Computational Biology·Yvonne Y LiArtem Cherkasov
Feb 20, 2009·Journal of Bioinformatics and Computational Biology·Nitin Bhardwaj, Hui Lu
Aug 7, 2007·Annual Review of Genetics·Kara Dolinski, David Botstein
Oct 12, 2012·International Journal of Evolutionary Biology·David A Fitzpatrick, Damien M O'Halloran
Nov 15, 2005·BMC Bioinformatics·Robin E C Lee, Lynn A Megeney
Mar 15, 2006·BMC Bioinformatics·Ramazan Saeed, Charlotte M Deane
Dec 2, 2006·BMC Bioinformatics·Caroline C Friedel, Ralf Zimmer
Mar 25, 2005·BMC Evolutionary Biology·Stefan Wuchty, Eivind Almaas
Jan 31, 2006·BMC Evolutionary Biology·Stefan WuchtyMichael T Ferdig
Mar 19, 2013·BMC Genomics·Piotr H PawlowskiPiotr Zielenkiewicz
Apr 24, 2008·Immunome Research·Csaba Ortutay, Mauno Vihinen
Nov 15, 2007·BMC Systems Biology·Kirill Evlampiev, Hervé Isambert
Jan 30, 2013·PLoS Computational Biology·Stefan WuchtyPeter O Bauer
May 8, 2014·Biochemical and Biophysical Research Communications·Lei YangWei Jiang
Apr 27, 2005·Proceedings of the National Academy of Sciences of the United States of America·Mónica Medina
Jun 1, 2007·Comparative and Functional Genomics·Luke HakesSimon C Lovell
Mar 30, 2005·The American Naturalist·Daniel Promislow

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