Protein complex evolution does not involve extensive network rewiring.

PLoS Computational Biology
Teunis J P van Dam, Berend Snel

Abstract

The formation of proteins into stable protein complexes plays a fundamental role in the operation of the cell. The study of the degree of evolutionary conservation of protein complexes between species and the evolution of protein-protein interactions has been hampered by lack of comprehensive coverage of the high-throughput (HTP) technologies that measure the interactome. We show that new high-throughput datasets on protein co-purification in yeast have a substantially lower false negative rate than previous datasets when compared to known complexes. These datasets are therefore more suitable to estimate the conservation of protein complex membership than hitherto possible. We perform comparative genomics between curated protein complexes from human and the HTP data in Saccharomyces cerevisiae to study the evolution of co-complex memberships. This analysis revealed that out of the 5,960 protein pairs that are part of the same complex in human, 2,216 are absent because both proteins lack an ortholog in S. cerevisiae, while for 1,828 the co-complex membership is disrupted because one of the two proteins lacks an ortholog. For the remaining 1,916 protein pairs, only 10% were never co-purified in the large-scale experiments. This i...Continue Reading

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Citations

May 29, 2014·PLoS Biology·Joseph A Marsh, Sarah A Teichmann
Feb 4, 2010·BMC Genomics·Adam J ReidChristine A Orengo
Jul 17, 2010·BMC Evolutionary Biology·Rita QuentalAntónio Amorim
Oct 5, 2010·PLoS Computational Biology·Juan A G RaneaChristine Orengo
Aug 24, 2011·Genome Biology and Evolution·Lisa G McFerrin, William R Atchley
Aug 25, 2011·BMC Systems Biology·Guy E ZinmanZiv Bar-Joseph
Nov 5, 2011·Nucleic Acids Research·Guilhem FaureRaphaël Guerois
Mar 19, 2013·BMC Genomics·Piotr H PawlowskiPiotr Zielenkiewicz
May 11, 2013·Genome Biology and Evolution·Colm J RyanGerard Cagney
Jan 28, 2012·Current Opinion in Plant Biology·Lee ChaeSeung Yon Rhee
Dec 1, 2012·Scientific Reports·Jinho KimSanguk Kim
Apr 4, 2013·Molecular Systems Biology·Xiaofeng XinGary D Bader
Dec 25, 2013·Molecular Systems Biology·Pedro BeltraoVera van Noort
Dec 11, 2014·Annual Review of Biochemistry·Joseph A Marsh, Sarah A Teichmann
Jul 5, 2013·PloS One·Robert Pesch, Ralf Zimmer
Jan 22, 2011·PLoS Computational Biology·Chong ShouMark B Gerstein
Feb 26, 2014·BMC Bioinformatics·Phi-Vu NguyenHon Wai Leong
Feb 26, 2010·Advances in Bioinformatics·Orhan CamoğluAmbuj K Singh

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Methods Mentioned

BETA
Y2H
Co-IP

Software Mentioned

Ensembl
Co
Linux
IP
BioMart
blast
XMLMakerFlattener
inparanoid
Reactome for Human
Perl scripts

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