Genome-scale modeling of yeast: chronology, applications and critical perspectives

Over the last 15 years, several genome-scale metabolic models (GSMMs) were developed for different yeast species, aiding both the elucidation of new biological processes and the shift toward a bio-based economy, through the design of in silico inspired cell factories. Here, an historical perspective of the GSMMs built over time for several yeast species is presented and the main inheritance patterns among the metabolic reconstructions are highlighted. We additionally provide a critical perspective on the overall genome-scale modeling procedure, underlining incomplete model validation and evaluation approaches and the quest for the integration of regulatory and kinetic information into yeast GSMMs. A summary of experimentally validated model-based metabolic engineering applications of yeast species is further emphasized, while the main challenges and future perspectives for the field are finally addressedThis work was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of a Ph.D. grant (PD/BD/52336/2013), of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01–0145FEDER-006684) and also in the context of the EU-funded initiative ERA-NET for Industrial Biotechnology (ERA-IB-2/0003/2013), in addition to the BioTecNorte operation (NORTE-01–0145FEDER-000004) funded by European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte.