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Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

View ORCID ProfileZachary D. Blount, View ORCID ProfileRohan Maddamsetti, Nkrumah A. Grant, Sumaya T. Ahmed, View ORCID ProfileTanush Jagdish, Brooke A. Sommerfeld, Alice Tillman, Jeremy Moore, View ORCID ProfileJoan L. Slonczewski, View ORCID ProfileJeffrey E. Barrick, View ORCID ProfileRichard E. Lenski
doi: https://doi.org/10.1101/2020.01.22.915975
Zachary D. Blount
1Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
2BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.
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  • For correspondence: zachary.david.blount@gmail.com rohan.maddamsetti@gmail.com
Rohan Maddamsetti
3Department of Biological Sciences, Old Dominion University, Norfolk, MA, USA.
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  • For correspondence: zachary.david.blount@gmail.com rohan.maddamsetti@gmail.com
Nkrumah A. Grant
1Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
2BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.
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Sumaya T. Ahmed
4Department of Biology, Kenyon College, Gambier, OH, USA.
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Tanush Jagdish
2BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.
5Program for Systems, Synthetic, and Quantitative Biology, Harvard University, Cambridge MA, USA.
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Brooke A. Sommerfeld
1Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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Alice Tillman
4Department of Biology, Kenyon College, Gambier, OH, USA.
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Jeremy Moore
4Department of Biology, Kenyon College, Gambier, OH, USA.
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Joan L. Slonczewski
4Department of Biology, Kenyon College, Gambier, OH, USA.
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  • ORCID record for Joan L. Slonczewski
Jeffrey E. Barrick
2BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.
6Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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Richard E. Lenski
1Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
2BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.
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ABSTRACT

Evolutionary innovations allow populations to colonize new, previously inaccessible ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in a population of Escherichia coli during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ can grow in citrate-only medium (DM0), which is a novel environment for E. coli. To study adaptation to this new niche, we evolved one set of Cit+ populations for 2,500 generations in DM0 and a control set in DM25. We identified numerous parallel mutations, many mediated by transposable elements. Several lineages evolved multi-copy amplifications containing the maeA gene, constituting up to ∼15% of the genome. We also found substantial cell death in ancestral and evolved clones. Our results demonstrate the importance of copy-number variation and transposable elements in the refinement of the Cit+ trait. However, the observed mortality suggests a persistent evolutionary mismatch between E. coli physiology and a citrate-only environment.

Footnotes

  • https://github.com/barricklab/LTEE-Ecoli

  • https://github.com/rohanmaddamsetti/DM0-evolution

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 23, 2020.
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Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment
Zachary D. Blount, Rohan Maddamsetti, Nkrumah A. Grant, Sumaya T. Ahmed, Tanush Jagdish, Brooke A. Sommerfeld, Alice Tillman, Jeremy Moore, Joan L. Slonczewski, Jeffrey E. Barrick, Richard E. Lenski
bioRxiv 2020.01.22.915975; doi: https://doi.org/10.1101/2020.01.22.915975
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Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment
Zachary D. Blount, Rohan Maddamsetti, Nkrumah A. Grant, Sumaya T. Ahmed, Tanush Jagdish, Brooke A. Sommerfeld, Alice Tillman, Jeremy Moore, Joan L. Slonczewski, Jeffrey E. Barrick, Richard E. Lenski
bioRxiv 2020.01.22.915975; doi: https://doi.org/10.1101/2020.01.22.915975

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