Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA) |
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Authors: | Juan A G Ranea Antonio Sillero Janet M Thornton Christine A Orengo |
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Institution: | (1) Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, London, WC1E 6BT, UK;(2) Departamento de Bioquimica, Instituto de Investigaciones Biomedicas Alberto Sols UAM/CSIC, Facultad de Medicina, Arzobispo Morcillo 4, 28029 Madrid, Spain;(3) EMBL-EBI, Wellcome Trust Genome Campus, Hinxto, Cambridge, CB10 1SD, UK |
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Abstract: | By exploiting three-dimensional structure comparison, which is more sensitive than conventional sequence-based methods for
detecting remote homology, we have identified a set of 140 ancestral protein domains using very restrictive criteria to minimize
the potential error introduced by horizontal gene transfer. These domains are highly likely to have been present in the Last
Universal Common Ancestor (LUCA) based on their universality in almost all of 114 completed prokaryotic (Bacteria and Archaea)
and eukaryotic genomes. Functional analysis of these ancestral domains reveals a genetically complex LUCA with practically
all the essential functional systems present in extant organisms, supporting the theory that life achieved its modern cellular
status much before the main kingdom separation (Doolittle 2000). In addition, we have calculated different estimations of the genetic and functional versatility of all the superfamilies
and functional groups in the prokaryote subsample. These estimations reveal that some ancestral superfamilies have been more
versatile than others during evolution allowing more genetic and functional variation. Furthermore, the differences in genetic
versatility between protein families are more attributable to their functional nature rather than the time that they have
been evolving. These differences in tolerance to mutation suggest that some protein families have eroded their phylogenetic
signal faster than others, hiding in many cases, their ancestral origin and suggesting that the calculation of 140 ancestral
domains is probably an underestimate.
Electronic Supplementary Material Electronic Supplementary material is available for this article at
and accessible for authorised users.
Reviewing Editor: Dr. Rafael Zarobya] |
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Keywords: | Last Universal Common Ancestor Ancestral protein families Genome comparison Protein evolution Evolutionary temperature Protein structural domains Ancestral protein functions |
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