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Journal of Molecular Evolution

, Volume 72, Issue 1, pp 14–33 | Cite as

Proteome Evolution and the Metabolic Origins of Translation and Cellular Life

  • Derek Caetano-Anollés
  • Kyung Mo Kim
  • Jay E. Mittenthal
  • Gustavo Caetano-Anollés
Article

Abstract

The origin of life has puzzled molecular scientists for over half a century. Yet fundamental questions remain unanswered, including which came first, the metabolic machinery or the encoding nucleic acids. In this study we take a protein-centric view and explore the ancestral origins of proteins. Protein domain structures in proteomes are highly conserved and embody molecular functions and interactions that are needed for cellular and organismal processes. Here we use domain structure to study the evolution of molecular function in the protein world. Timelines describing the age and function of protein domains at fold, fold superfamily, and fold family levels of structural complexity were derived from a structural phylogenomic census in hundreds of fully sequenced genomes. These timelines unfold congruent hourglass patterns in rates of appearance of domain structures and functions, functional diversity, and hierarchical complexity, and revealed a gradual build up of protein repertoires associated with metabolism, translation and DNA, in that order. The most ancient domain architectures were hydrolase enzymes and the first translation domains had catalytic functions for the aminoacylation and the molecular switch-driven transport of RNA. Remarkably, the most ancient domains had metabolic roles, did not interact with RNA, and preceded the gradual build-up of translation. In fact, the first translation domains had also a metabolic origin and were only later followed by specialized translation machinery. Our results explain how the generation of structure in the protein world and the concurrent crystallization of translation and diversified cellular life created further opportunities for proteomic diversification.

Keywords

Origin of life Phylogenetic analysis Protein domain structure Ribonucleoprotein world RNA world 

Abbreviations

aRS

Aminoacyl-tRNA synthetase

F

Fold

FSF

Fold superfamily

FF

Fold family

Nd

Node distance

r-Protein

Ribosomal protein

SCOP

Structural classification of proteins

Notes

Acknowledgments

A substantial portion of this work is part of DCA’s undergraduate thesis. We thank Ajith Harish and Feng-Jie Sun for providing data on RNA-protein interactions, Minglei Wang for phylogenomic reconstruction, and Rakhee Kalelkar for help with construction of Z-diagrams. Research was supported by the National Science Foundation (MCB-0749836), the Illinois C-FAR program, CREES-USDA, and the International Atomic Energy Agency in Vienna. Any opinions, findings, and conclusions and recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funding agencies.

Supplementary material

239_2010_9400_MOESM1_ESM.pdf (734 kb)
Supplementary material 1 (PDF 733 kb)

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Derek Caetano-Anollés
    • 1
    • 2
  • Kyung Mo Kim
    • 1
  • Jay E. Mittenthal
    • 3
  • Gustavo Caetano-Anollés
    • 1
  1. 1.Evolutionary Bioinformatics Laboratory, Department of Crop SciencesUniversity of IllinoisUrbanaUSA
  2. 2.School of Molecular and Cellular BiologyUniversity of IllinoisUrbanaUSA
  3. 3.Department of Cell and Developmental BiologyUniversity of IllinoisUrbanaUSA

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