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Comparative evolutionary analysis of protein complexes in E. coli and yeast

Reid, AJ; Ranea, JAG; Orengo, CA; (2010) Comparative evolutionary analysis of protein complexes in E. coli and yeast. BMC GENOMICS , 11 , Article 79. 10.1186/1471-2164-11-79. Green open access

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Abstract

Background: Proteins do not act in isolation; they frequently act together in protein complexes to carry out concerted cellular functions. The evolution of complexes is poorly understood, especially in organisms other than yeast, where little experimental data has been available.Results: We generated accurate, high coverage datasets of protein complexes for E. coli and yeast in order to study differences in the evolution of complexes between these two species. We show that substantial differences exist in how complexes have evolved between these organisms. A previously proposed model of complex evolution identified complexes with cores of interacting homologues. We support findings of the relative importance of this mode of evolution in yeast, but find that it is much less common in E. coli. Additionally it is shown that those homologues which do cluster in complexes are involved in eukaryote-specific functions. Furthermore we identify correlated pairs of non-homologous domains which occur in multiple protein complexes. These were identified in both yeast and E. coli and we present evidence that these too may represent complex cores in yeast but not those of E. coli.Conclusions: Our results suggest that there are differences in the way protein complexes have evolved in E. coli and yeast. Whereas some yeast complexes have evolved by recruiting paralogues, this is not apparent in E. coli. Furthermore, such complexes are involved in eukaryotic-specific functions. This implies that the increase in gene family sizes seen in eukaryotes in part reflects multiple family members being used within complexes. However, in general, in both E. coli and yeast, homologous domains are used in different complexes.

Type: Article
Title: Comparative evolutionary analysis of protein complexes in E. coli and yeast
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/1471-2164-11-79
Publisher version: http://dx.doi.org10.1186/1471-2164-11-79
Language: English
Additional information: © 2010 Reid et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: INTERACTION NETWORKS, ESCHERICHIA-COLI, SACCHAROMYCES-CEREVISIAE, FUNCTIONAL MODULES, SEMANTIC SIMILARITY, GENE ONTOLOGY, ANNOTATION, GENOME, DUPLICATION, EUKARYOTES
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology
URI: https://discovery.ucl.ac.uk/id/eprint/1299033
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