Protein complex evolution does not involve extensive network rewiring.

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 covera...

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Autores principales:	Teunis J P van Dam, Berend Snel
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/ff23b9f60d5842099f65602d87eced73
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spelling	oai:doaj.org-article:ff23b9f60d5842099f65602d87eced732021-11-25T05:41:12ZProtein complex evolution does not involve extensive network rewiring.1553-734X1553-735810.1371/journal.pcbi.1000132https://doaj.org/article/ff23b9f60d5842099f65602d87eced732008-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18711636/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The 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 implies a conservation level of co-complex membership of 90% when the genes coding for the protein pairs that participate in the same protein complex are also conserved. We conclude that the evolutionary dynamics of protein complexes are, by and large, not the result of network rewiring (i.e. acquisition or loss of co-complex memberships), but mainly due to genomic acquisition or loss of genes coding for subunits. We thus reveal evidence for the tight interrelation of genomic and network evolution.Teunis J P van DamBerend SnelPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 4, Iss 7, p e1000132 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Teunis J P van Dam Berend Snel Protein complex evolution does not involve extensive network rewiring.
description	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 implies a conservation level of co-complex membership of 90% when the genes coding for the protein pairs that participate in the same protein complex are also conserved. We conclude that the evolutionary dynamics of protein complexes are, by and large, not the result of network rewiring (i.e. acquisition or loss of co-complex memberships), but mainly due to genomic acquisition or loss of genes coding for subunits. We thus reveal evidence for the tight interrelation of genomic and network evolution.
format	article
author	Teunis J P van Dam Berend Snel
author_facet	Teunis J P van Dam Berend Snel
author_sort	Teunis J P van Dam
title	Protein complex evolution does not involve extensive network rewiring.
title_short	Protein complex evolution does not involve extensive network rewiring.
title_full	Protein complex evolution does not involve extensive network rewiring.
title_fullStr	Protein complex evolution does not involve extensive network rewiring.
title_full_unstemmed	Protein complex evolution does not involve extensive network rewiring.
title_sort	protein complex evolution does not involve extensive network rewiring.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/ff23b9f60d5842099f65602d87eced73
work_keys_str_mv	AT teunisjpvandam proteincomplexevolutiondoesnotinvolveextensivenetworkrewiring AT berendsnel proteincomplexevolutiondoesnotinvolveextensivenetworkrewiring
_version_	1718414557125279744

Protein complex evolution does not involve extensive network rewiring.

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