Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication

PLoS Biol. 2012;10(12):e1001446. doi: 10.1371/journal.pbio.1001446. Epub 2012 Dec 11.

Abstract

Gene duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. Here, we study a large family of fungal glucosidase genes that underwent several duplication events. We reconstruct all key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence of these duplicated enzymes and show that whereas the classic models of dosage, sub-, and neofunctionalization are helpful to conceptualize the implications of gene duplication, the three mechanisms co-occur and intertwine.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / genetics
  • Binding Sites
  • Evolution, Molecular*
  • Fungal Proteins / genetics
  • Gene Dosage / drug effects
  • Gene Duplication* / drug effects
  • Genes, Duplicate / genetics
  • Glucosides / pharmacology
  • Hydrolysis / drug effects
  • Maltose / metabolism
  • Models, Molecular
  • Multigene Family / genetics
  • Saccharomyces cerevisiae / drug effects
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / growth & development
  • Selection, Genetic
  • Substrate Specificity / drug effects
  • alpha-Glucosidases / genetics*

Substances

  • Amino Acids
  • Fungal Proteins
  • Glucosides
  • Maltose
  • alpha-Glucosidases

Grant support

S. Maere and K. Vanneste are fellows of the Fund for Scientific Research-Flanders (FWO). Research in the lab of KJV is supported by the Human Frontier Science Program, ERC Starting Grant 241426, VIB, EMBO YIP program, KU Leuven, FWO, IWT and the AB InBev Baillet-Latour foundation. Research in the lab of SM is supported by VIB, Ghent University, FWO and IWT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.