The evolutionary plasticity of chromosome metabolism allows adaptation to constitutive DNA replication stress

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Abstract

Many biological features are conserved and thus considered to be resistant to evolutionary change. While rapid genetic adaptation following the removal of conserved genes has been observed, we often lack a mechanistic understanding of how adaptation happens. We used the budding yeast, Saccharomyces cerevisiae, to investigate the evolutionary plasticity of chromosome metabolism, a network of evolutionary conserved modules. We experimentally evolved cells constitutively experiencing DNA replication stress caused by the absence of Ctf4, a protein that coordinates the enzymatic activities at replication forks. Parallel populations adapted to replication stress, over 1000 generations, by acquiring multiple, concerted mutations. These mutations altered conserved features of two chromosome metabolism modules, DNA replication and sister chromatid cohesion, and inactivated a third, the DNA damage checkpoint. The selected mutations define a functionally reproducible evolutionary trajectory. We suggest that the evolutionary plasticity of chromosome metabolism has implications for genome evolution in natural populations and cancer.

Data availability

A major dataset, containing the sequencing data used in the manuscript has been made publicly available at the EBI European Nucleotide Archive (Accession no: PRJEB34641)

The following data sets were generated

1. Fumasoni M
2. Murray AW
(2019) Sequences from The evolutionary plasticity of chromosome metabolism allows adaptation to constitutive DNA replication stress
EBI European Nucleotide Archive, PRJEB34641.

http://www.ebi.ac.uk/ ena/data/view/ PRJEB34641

Article and author information

Author details

Marco Fumasoni

Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States

For correspondence
marcofumasoni@fas.harvard.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4507-7824
Andrew W Murray

Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-0868-6604

Funding

Human Frontier Science Program (LT000786/2016-L)

Marco Fumasoni

European Molecular Biology Organization (ALTF 485-2015)

Marco Fumasoni

Fondazione AIRC per la ricerca sul cancro (iCARE 17957)

Marco Fumasoni

National Institute of General Medical Sciences (RO1-GM43987)

Andrew W Murray

NSF-Simons Center for Mathematical and Statistical Analysis of Biology at Harvard (#1764269)

Andrew W Murray

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.