Accelerating Pathway Evolution by Increasing the Gene Dosage of Chromosomal Segments

Gregg Beckham, Payal Khanna, Jeffrey Linger, Christopher Johnson, Melissa Tumen-Velasquez, Alaa Ahmed, Alicia Schmidt, Ellen Neidle, Sarah Lee, Mark Eiteman, Graham Dominick, Emily Fulk

Research output: Contribution to journalArticlepeer-review

42 Scopus Citations

Abstract

Experimental evolution is a critical tool in many disciplines, including metabolic engineering and synthetic biology. However, current methods rely on the chance occurrence of a key step that can dramatically accelerate evolution in natural systems, namely increased gene dosage. Our studies sought to induce the targeted amplification of chromosomal segments to facilitate rapid evolution. Since increased gene dosage confers novel phenotypes and genetic redundancy, we developed a method, Evolution by Amplification and Synthetic Biology (EASy), to create tandem arrays of chromosomal regions. In Acinetobacter baylyi, EASy was demonstrated on an important bioenergy problem, the catabolism of lignin-derived aromatic compounds. The initial focus on guaiacol (2-methoxyphenol), a common lignin degradation product, led to the discovery of Amycolatopsis genes (gcoAB) encoding a cytochrome P450 enzyme that converts guaiacol to catechol. However, chromosomal integration of gcoAB in Pseudomonas putida or A. baylyi did not enable guaiacol to be used as the sole carbon source despite catechol being a growth substrate. In ∼1,000 generations, EASy yielded alleles that in single chromosomal copy confer growth on guaiacol. Different variants emerged, including fusions between GcoA and CatA (catechol 1,2-dioxygenase). This study illustrates the power of harnessing chromosomal gene amplification to accelerate the evolution of desirable traits.

Original languageAmerican English
Pages (from-to)7105-7110
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume115
Issue number27
DOIs
StatePublished - 2018

Bibliographical note

Publisher Copyright:
© 2018 National Academy of Sciences. All Rights Reserved.

NREL Publication Number

  • NREL/JA-5100-71408

Keywords

  • Acinetobacter
  • Evolution
  • Gene amplification
  • Guaiacol
  • P450

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