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A prototrophic deletion mutant collection for yeast metabolomics and systems biology

Nature Biotechnology volume 30, pages 1176–1178 (2012)Cite this article

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Auxotrophic markers—mutations in genes encoding enzymes in pathways for the biosynthesis of metabolic building blocks, such as amino acids or nucleotides—are used as selection markers in most yeast genetics and genomics experiments1,2,3. The nutritional deficiency caused by the mutation (auxotrophy) can be compensated by supplying the required nutrient in the growth medium. This compensation, however, is not necessarily quantitative because such mutations influence several physiological parameters and may act in combination2,4,5. The construction of a prototrophic derivative of the parent strain of the widely used genome-scale yeast deletion collection1 has confirmed the need to remove auxotrophic markers to reduce bias in physiological and metabolic studies2. Moreover, flux balance analyses using a genome-wide metabolic model (Yeast 5)6 indicate that the activity status of some 200–300 reactions changes between different auxotrophic strains and the wild type. To alleviate this bias, we have constructed a version of the haploid deletant collection restoring prototrophy in the genetic background and thus preventing any influence of auxotrophy on the phenotype of a given gene deletion. This new deletant library is based on the popular S228c (MATa) knock-out collection1, and facilitates the exploitation of prototrophic yeast in both functional genomics and quantitative systems biology.

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Figure 1: The combinatorial impact of yeast auxotrophic markers on yeast physiology.

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Author notes

  1. Michael Mülleder and Floriana Capuano: These authors contributed equally to this work.

Authors and Affiliations

  1. Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, UK

    Michael Mülleder, Floriana Capuano, Pınar Pir, Stephen G Oliver & Markus Ralser

  2. Institute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland

    Stefan Christen & Uwe Sauer

Authors
  1. Michael Mülleder
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  2. Floriana Capuano
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  3. Pınar Pir
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  4. Stefan Christen
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  5. Uwe Sauer
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  6. Stephen G Oliver
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  7. Markus Ralser
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Corresponding author

Correspondence to Markus Ralser.

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The authors declare no competing financial interests.

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Supplementary Figures 1–3 Supplementary Tables 1–2, Supplementary Methods (PDF 1246 kb)

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Mülleder, M., Capuano, F., Pir, P. et al. A prototrophic deletion mutant collection for yeast metabolomics and systems biology. Nat Biotechnol 30, 1176–1178 (2012). https://doi.org/10.1038/nbt.2442

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