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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

Abstract

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.

Keywords:

  • 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