Adaptive evolution of a minimal organism with a synthetic genome

Troy E. Sandberg; Kim S. Wise; Christopher Dalldorf; Richard Szubin; Adam M. Feist; John I. Glass; Bernhard O. Palsson

iScience (Sep 2023)

Adaptive evolution of a minimal organism with a synthetic genome

Troy E. Sandberg,
Kim S. Wise,
Christopher Dalldorf,
Richard Szubin,
Adam M. Feist,
John I. Glass,
Bernhard O. Palsson

Affiliations

Troy E. Sandberg: Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
Kim S. Wise: J. Craig Venter Institute, San Diego, La Jolla, CA, USA
Christopher Dalldorf: Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
Richard Szubin: Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
Adam M. Feist: Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
John I. Glass: J. Craig Venter Institute, San Diego, La Jolla, CA, USA
Bernhard O. Palsson: Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark; Corresponding author

Journal volume & issue: Vol. 26, no. 9
p. 107500

Abstract

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Summary: The bacterial strain JCVI-syn3.0 stands as the first example of a living organism with a minimized synthetic genome, derived from the Mycoplasma mycoides genome and chemically synthesized in vitro. Here, we report the experimental evolution of a syn3.0- derived strain. Ten independent replicates were evolved for several hundred generations, leading to growth rate improvements of > 15%. Endpoint strains possessed an average of 8 mutations composed of indels and SNPs, with a pronounced C/G- > A/T transversion bias. Multiple genes were repeated mutational targets across the independent lineages, including phase variable lipoprotein activation, 5 distinct; nonsynonymous substitutions in the same membrane transporter protein, and inactivation of an uncharacterized gene. Transcriptomic analysis revealed an overall tradeoff reflected in upregulated ribosomal proteins and downregulated DNA and RNA related proteins during adaptation. This work establishes the suitability of synthetic, minimal strains for laboratory evolution, providing a means to optimize strain growth characteristics and elucidate gene functionality.

Published in iScience

ISSN: 2589-0042 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science
Website: http://www.cell.com/iscience/home

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