Yeast Genome-Scale Metabolic Models for Simulating Genotype-Phenotype Relations

Sandra Castillo, Kiran Raosaheb Patil, Paula Jouhten

Research output: Chapter in Book/Report/Conference proceedingChapter or book articleScientificpeer-review

Abstract

Understanding genotype-phenotype dependency is a universal aim for all life sciences. While the complete genotype-phenotype relations remain challenging to resolve, metabolic phenotypes are moving within the reach through genome-scale metabolic model simulations. Genome-scale metabolic models are available for commonly investigated yeasts, such as model eukaryote and domesticated fermentation species Saccharomyces cerevisiae, and automatic reconstruction methods facilitate obtaining models for any sequenced species. The models allow for investigating genotype-phenotype relations through simulations simultaneously considering the effects of nutrient availability, and redox and energy homeostasis in cells. Genome-scale models also offer frameworks for omics data integration to help to uncover how the translation of genotypes to the apparent phenotypes is regulated at different levels. In this chapter, we provide an overview of the yeast genome-scale metabolic models and the simulation approaches for using these models to interrogate genotype-phenotype relations. We review the methodological approaches according to the underlying biological reasoning in order to inspire formulating novel questions and applications that the genome-scale metabolic models could contribute to. Finally, we discuss current challenges and opportunities in the genome-scale metabolic model simulations.

Original languageEnglish
Title of host publicationYeasts in Biotechnology and Human Health
EditorsI. Sá-Correia
PublisherSpringer
Pages111-133
Number of pages23
Volume58
ISBN (Electronic)978-3-030-13035-0
ISBN (Print)978-3-030-13034-3
DOIs
Publication statusPublished - 2019
MoE publication typeA3 Part of a book or another research book

Publication series

NameProgress in molecular and subcellular biology
PublisherSpringer
ISSN (Print)0079-6484

Fingerprint

Yeasts
Genotype
Genome
Phenotype
Biological Science Disciplines
Eukaryota
Fermentation
Oxidation-Reduction
Saccharomyces cerevisiae
Homeostasis
Food

Keywords

  • Genome-scale metabolic model
  • Genotype–phenotype dependency
  • Metabolic flux
  • Strain design
  • Yeast metabolism

Cite this

Castillo, S., Patil, K. R., & Jouhten, P. (2019). Yeast Genome-Scale Metabolic Models for Simulating Genotype-Phenotype Relations. In I. Sá-Correia (Ed.), Yeasts in Biotechnology and Human Health (Vol. 58, pp. 111-133). Springer. Progress in molecular and subcellular biology https://doi.org/10.1007/978-3-030-13035-0_5
Castillo, Sandra ; Patil, Kiran Raosaheb ; Jouhten, Paula. / Yeast Genome-Scale Metabolic Models for Simulating Genotype-Phenotype Relations. Yeasts in Biotechnology and Human Health. editor / I. Sá-Correia. Vol. 58 Springer, 2019. pp. 111-133 (Progress in molecular and subcellular biology).
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Castillo, S, Patil, KR & Jouhten, P 2019, Yeast Genome-Scale Metabolic Models for Simulating Genotype-Phenotype Relations. in I Sá-Correia (ed.), Yeasts in Biotechnology and Human Health. vol. 58, Springer, Progress in molecular and subcellular biology, pp. 111-133. https://doi.org/10.1007/978-3-030-13035-0_5

Yeast Genome-Scale Metabolic Models for Simulating Genotype-Phenotype Relations. / Castillo, Sandra; Patil, Kiran Raosaheb; Jouhten, Paula.

Yeasts in Biotechnology and Human Health. ed. / I. Sá-Correia. Vol. 58 Springer, 2019. p. 111-133 (Progress in molecular and subcellular biology).

Research output: Chapter in Book/Report/Conference proceedingChapter or book articleScientificpeer-review

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Castillo S, Patil KR, Jouhten P. Yeast Genome-Scale Metabolic Models for Simulating Genotype-Phenotype Relations. In Sá-Correia I, editor, Yeasts in Biotechnology and Human Health. Vol. 58. Springer. 2019. p. 111-133. (Progress in molecular and subcellular biology). https://doi.org/10.1007/978-3-030-13035-0_5