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Parallel changes in gene essentiality over 50,000 generations of evolution

View ORCID ProfileAnurag Limdi, View ORCID ProfileSiân V. Owen, View ORCID ProfileCristina Herren, View ORCID ProfileRichard E. Lenski, View ORCID ProfileMichael Baym
doi: https://doi.org/10.1101/2022.05.17.492023
Anurag Limdi
1Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
2Molecules, Cells, and Organisms Graduate Program, Harvard University, Cambridge, Massachusetts 02138, USA
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Siân V. Owen
1Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Cristina Herren
1Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
3Harvard Data Science Initiative, Harvard University, Boston, Massachusetts 02115, USA
4Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts 02115, USA
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Richard E. Lenski
5Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
6Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan 48824, USA
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Michael Baym
1Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
3Harvard Data Science Initiative, Harvard University, Boston, Massachusetts 02115, USA
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  • For correspondence: baym@hms.harvard.edu
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Abstract

Over evolutionary time, bacteria face changing environments, which may require different sets of genes for survival. As they adapt to a specific constant environment, some genes are modified and lost, which can increase fitness while also modulating the effects of further gene losses. However, whether evolutionary specialization leads to systematic changes in robustness to gene loss is largely unexplored. Here, we compare the effects of insertion mutations in Escherichia coli between ancestral and 12 independently derived strains after 50,000 generations of growth in a simple, uniform environment. We find that epistasis between insertion mutations and genetic background is common, but the overall distribution of fitness effects is largely unchanged. In particular, we see systematic changes in gene essentiality, with more genes becoming essential over evolution than vice versa. The resulting changes often occurred in parallel across the independently evolving populations. A few of the changes in gene essentiality are associated with large structural variations, but most are not. Taken together, our results demonstrate that gene essentiality is a dynamic, evolvable property, and they suggest that changes in gene essentiality are a result of natural selection in this long-term evolution experiment, rather than a mere byproduct of structural changes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/baymlab/2022_Limdi-TnSeq-LTEE

  • https://doi.org/10.5281/zenodo.6547536

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 4.0 International license.
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Posted May 17, 2022.
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Parallel changes in gene essentiality over 50,000 generations of evolution
Anurag Limdi, Siân V. Owen, Cristina Herren, Richard E. Lenski, Michael Baym
bioRxiv 2022.05.17.492023; doi: https://doi.org/10.1101/2022.05.17.492023
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Parallel changes in gene essentiality over 50,000 generations of evolution
Anurag Limdi, Siân V. Owen, Cristina Herren, Richard E. Lenski, Michael Baym
bioRxiv 2022.05.17.492023; doi: https://doi.org/10.1101/2022.05.17.492023

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