Laboratory evolution of a biotin-requiring Saccharomyces cerevisiae strain for full biotin prototrophy and identification of causal mutations

Laboratory evolution of a biotin-requiring Saccharomyces cerevisiae strain for full biotin prototrophy and identification of causal mutations

Bracher, J.M. (TU Delft BT/Industriele Microbiologie)
de Hulster, A.F. (TU Delft BT/Industriele Microbiologie)
Koster, C.C. (TU Delft BT/Industriele Microbiologie)
van den Broek, M.A. (TU Delft BT/Industriele Microbiologie)
Daran, J.G. (TU Delft BT/Industriele Microbiologie)
van Maris, A.J.A. (TU Delft BT/Industriele Microbiologie)
Pronk, J.T. (TU Delft BT/Industriele Microbiologie)

2017-08-01

Biotin prototrophy is a rare, incompletely understood, and industrially relevant characteristic of Saccharomyces cerevisiae strains. The genome of the haploid laboratory strain CEN.PK113-7D contains a full complement of biotin biosynthesis genes, but its growth in biotin-free synthetic medium is extremely slow (specific growth rate [μ] ≈ 0.01 h^-1). Four independent evolution experiments in repeated batch cultures and accelerostats yielded strains whose growth rates (μ ≤ 0.36 h^-1) in biotin-free and biotin-supplemented media were similar. Whole-genome resequencing of these evolved strains revealed up to 40-fold amplification of BIO1, which encodes pimeloyl-coenzyme A (CoA) synthetase. The additional copies of BIO1 were found on different chromosomes, and its amplification coincided with substantial chromosomal rearrangements. A key role of this gene amplification was confirmed by overexpression of BIO1 in strain CEN.PK113-7D, which enabled growth in biotin-free medium (μ= 0.15 h^-1). Mutations in the membrane transporter genes TPO1 and/or PDR12 were found in several of the evolved strains. Deletion of TPO1 and PDR12 in a BIO1-overexpressing strain increased its specific growth rate to 0.25 h^-1. The effects of null mutations in these genes, which have not been previously associated with biotin metabolism, were nonadditive. This study demonstrates that S. cerevisiae strains that carry the basic genetic information for biotin synthesis can be evolved for full biotin prototrophy and identifies new targets for engineering biotin prototrophy into laboratory and industrial strains of this yeast.

Adaptive laboratory evolution
Biotin
Prototrophy
Reverse metabolic engineering
Saccharomyces cerevisiae
Vitamin biosynthesis
Whole-genome sequencing

http://resolver.tudelft.nl/uuid:8cb1a309-0454-459c-a1f5-0d43b2dfd5fb

https://doi.org/10.1128/AEM.00892-17

0099-2240

Applied and Environmental Microbiology, 83 (16), 1-16

Institutional Repository

journal article

© 2017 J.M. Bracher, A.F. de Hulster, C.C. Koster, M.A. van den Broek, J.G. Daran, A.J.A. van Maris, J.T. Pronk