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Universal Sharing Patterns in Proteomes and Evolution of Protein Fold Architecture and Life

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Abstract

Protein evolution is imprinted in both the sequence and the structure of evolutionary building blocks known as protein domains. These domains share a common ancestry and can be unified into a comparatively small set of folding architectures, the protein folds. We have traced the distribution of protein folds between and within proteomes belonging to Eukarya, Archaea, and Bacteria along the branches of a universal phylogeny of protein architecture. This tree was reconstructed from global fold-usage statistics derived from a structural census of proteomes. We found that folds shared by the three organismal domains were placed almost exclusively at the base of the rooted tree and that there were marked heterogeneities in fold distribution and clear evolutionary patterns related to protein architecture and organismal diversification. These include a relative timing for the emergence of prokaryotes, congruent episodes of architectural loss and diversification in Archaea and Bacteria, and a late and quite massive rise of architectural novelties in Eukarya perhaps linked to multicellularity.

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Acknowledgments

We would like to thank Jay Mittenthal (University of Illinois) and Dietz Bauer (Ohio State University) for valuable comments and suggestions.

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  1. Department of Crop Sciences, University of Illinois, 332 NSRC, 1101 West Peabody Drive, Urbana, IL, 61801, USA

    Gustavo Caetano-Anollés

  2. Vital NRG, Knoxville, TN, 37919, USA

    Derek Caetano-Anollés

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Correspondence to Gustavo Caetano-Anollés.

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Caetano-Anollés, G., Caetano-Anollés, D. Universal Sharing Patterns in Proteomes and Evolution of Protein Fold Architecture and Life. J Mol Evol 60, 484–498 (2005). https://doi.org/10.1007/s00239-004-0221-6

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