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Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts

Author

Listed:
  • Tyler W. Doughty

    (Chalmers University of Technology
    Chalmers University of Technology)

  • Iván Domenzain

    (Chalmers University of Technology
    Chalmers University of Technology)

  • Aaron Millan-Oropeza

    (Université Paris-Saclay)

  • Noemi Montini

    (University College Cork)

  • Philip A. Groot

    (Delft University of Technology, Van der Maasweg 9)

  • Rui Pereira

    (Chalmers University of Technology
    Chalmers University of Technology)

  • Jens Nielsen

    (Chalmers University of Technology
    Chalmers University of Technology)

  • Céline Henry

    (Université Paris-Saclay)

  • Jean-Marc G. Daran

    (Delft University of Technology, Van der Maasweg 9)

  • Verena Siewers

    (Chalmers University of Technology
    Chalmers University of Technology)

  • John P. Morrissey

    (University College Cork)

Abstract

The Saccharomycotina subphylum (budding yeasts) spans 400 million years of evolution and includes species that thrive in diverse environments. To study niche-adaptation, we identify changes in gene expression in three divergent yeasts grown in the presence of various stressors. Duplicated and non-conserved genes are significantly more likely to respond to stress than genes that are conserved as single-copy orthologs. Next, we develop a sorting method that considers evolutionary origin and duplication timing to assign an evolutionary age to each gene. Subsequent analysis reveals that genes that emerged in recent evolutionary time are enriched amongst stress-responsive genes for each species. This gene expression pattern suggests that budding yeasts share a stress adaptation mechanism, whereby selective pressure leads to functionalization of young genes to improve growth in adverse conditions. Further characterization of young genes from species that thrive in harsh environments can inform the design of more robust strains for biotechnology.

Suggested Citation

  • Tyler W. Doughty & Iván Domenzain & Aaron Millan-Oropeza & Noemi Montini & Philip A. Groot & Rui Pereira & Jens Nielsen & Céline Henry & Jean-Marc G. Daran & Verena Siewers & John P. Morrissey, 2020. "Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16073-3
    DOI: 10.1038/s41467-020-16073-3
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    Cited by:

    1. Alexander Kroll & Yvan Rousset & Xiao-Pan Hu & Nina A. Liebrand & Martin J. Lercher, 2023. "Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Iván Domenzain & Benjamín Sánchez & Mihail Anton & Eduard J. Kerkhoven & Aarón Millán-Oropeza & Céline Henry & Verena Siewers & John P. Morrissey & Nikolaus Sonnenschein & Jens Nielsen, 2022. "Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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