Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations

Kang Kang, Basti Bergdahl, Daniel Machado, Laura Dato, Ting-Li Han, Jun Li, Silas Villas-Boas, Markus J Herrgård, Jochen Förster*, Gianni Panagiotou

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

147 Downloads (Pure)

Abstract

The selection of bioengineering platform strains and engineering strategies to improve the stress resistance of Saccharomyces cerevisiae remains a pressing need in bio-based chemical production. Thus, a systematic effort to exploit genotypic and phenotypic diversity to boost yeast's industrial value is still urgently needed. We analyzed 5,400 growth curves obtained from 36 S. cerevisiae strains and comprehensively profiled their resistances against 13 industrially relevant stresses. We observed that bioethanol and brewing strains exhibit higher resistance against acidic conditions; however, plant isolates tend to have a wider range of resistance, which may be associated with their metabolome and fluxome signatures in the tricarboxylic acid cycle and fatty acid metabolism. By deep genomic sequencing, we found that industrial strains have more genomic duplications especially affecting transcription factors, showing that they result from disparate evolutionary paths in comparison with the environmental strains, which have more indels, gene deletions, and strain-specific genes. Genome-wide association studies coupled with protein-protein interaction networks uncovered novel genetic determinants of stress resistances. These resistance-related engineering targets and strain rankings provide a valuable source for engineering significantly improved industrial platform strains.
Original languageEnglish
Article numbergiz015
JournalGigaScience
Volume8
Issue number4
ISSN2047-217X
DOIs
Publication statusPublished - 2019

Keywords

  • Saccharomyces cerevisiae
  • geno-to-phenotype association
  • multi-omic study
  • platform strain
  • stress resistance

Cite this

Kang, K., Bergdahl, B., Machado, D., Dato, L., Han, T-L., Li, J., Villas-Boas, S., Herrgård, M. J., Förster, J., & Panagiotou, G. (2019). Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations. GigaScience, 8(4), [giz015]. https://doi.org/10.1093/gigascience/giz015