Distribution of protein folds in the tree of life.

Abstract :

To reconstruct the Tree of Life, protein and DNA sequences have been used for long, but a level of protein 3D structural organization has been neglected, fold. Folds are defined as the architecture and topology of secondary structures. 1,232 of these have been characterized. We have mapped the folds onto a tree of life and measured the consistency of each fold as a character in this tree. As a result, 20% of the folds are present in all superkingdoms, and 53.9% are potential synapomorphies. We find fold characters consistently supporting several nested eukaryotic clades with divergence times spanning from 1,100 mya to 380 mya. As for the earliest branches of the tree of life, the three superkingdoms are discriminated by eukaryotic specific folds (181) as well as shared folds between Eukaryota and one of the two other superkingdoms. Many folds shared by parts of eukaryotes and some eubacteria should result from past horizontal transfers (e.g. cyanobacteria to photosynthetic eukaryotes) witnessing significant fold flow to eukaryotes. Among eukaryotes, some folds therefore appear as synapomorphies of the species phylogeny, while others are markers of transfers to Eukaryota.

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