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Evolution of the Protein Repertoire

Systems Biology

  1. Aaron David Goldman1,2,
  2. Jeremy A. Horst3,4,
  3. Ling-Hong Hung4,
  4. Ram Samudrala4

Published Online: 15 MAY 2012

DOI: 10.1002/3527600906.mcb.200400157.pub2

Reviews in Cell Biology and Molecular Medicine

Reviews in Cell Biology and Molecular Medicine

How to Cite

Goldman, A. D., Horst, J. A., Hung, L.-H. and Samudrala, R. 2012. Evolution of the Protein Repertoire. Reviews in Cell Biology and Molecular Medicine. .

Author Information

  1. 1

    Princeton University, Department of Ecology and Evolutionary Biology, Princeton, NJ, USA

  2. 2

    NASA Astrobiology Institute, Center for Ribosomal Origins and Evolution at Georgia Institute of Technology, NASA Postdoctoral Program, Atlanta, GA, USA

  3. 3

    University of California San Francisco School of Pediatric Dentistry, Department of Orofacial Sciences, San Francisco, CA, USA

  4. 4

    University of Washington, Department of Microbiology, Seattle, WA, USA

Publication History

  1. Published Online: 15 MAY 2012


A protein is at once the translation product of a gene, a polymer of amino acids folded in three-dimensional space, a molecular machine imparting a function, and a small – but often critical – component of the cell's physiology. Each of these facets of a protein is inherently linked to the others; yet, each is impacted by evolutionary processes differently. The evolution of the protein repertoire involves a broad variety of phenomena, many of which are understood in considerable detail. The aim of this chapter is to provide a panoramic survey of the subject, and to relate the molecular mechanisms of evolution to their effects on proteins, the genes that encode them, and the physiological networks that they populate.


  • Allosteric regulation;
  • Convergent evolution;
  • Cooperativity;
  • Directed evolution;
  • Divergent evolution;
  • Gene cluster;
  • Gene duplication;
  • Homolog;
  • Homologous recombination;
  • Horizontal gene transfer;
  • Metabolic network;
  • Metabolic pathway;
  • Metabolome;
  • Multiprotein complex;
  • Neofunctionalization;
  • Nonsynonymous substitution;
  • Operon;
  • Ortholog;
  • Paralog;
  • Phylogenomics;
  • Phylogeny;
  • Point mutation;
  • Protein domain;
  • Protein primary structure;
  • Protein quaternary structure;
  • Protein repertoire;
  • Protein secondary structure;
  • Protein tertiary structure;
  • Protein–protein interaction network;
  • Proteome;
  • Pseudogene;
  • Regulatory network;
  • Subfunctionalization;
  • Synonymous substitution;
  • Trans-splicing;
  • Transcriptome