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

    4 Citations (Scopus)

    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

    SeriesProgress in molecular and subcellular biology
    ISSN0079-6484

    Keywords

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

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