Universal sharing patterns in proteomes and evolution of protein fold architecture and life

Gustavo Caetano-Anollés, Derek Caetano-Anollés

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)484-498
Number of pages15
JournalJournal of Molecular Evolution
Issue number4
StatePublished - Apr 2005


  • Archaea
  • Bacteria
  • Eukarya
  • Organismal diversification
  • Origins of life
  • Phylogenetic tracing
  • Protein structure
  • Proteome diversification

ASJC Scopus subject areas

  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology


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