Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community
Genome-scale metabolic models (GEMs) can facilitate metabolism-focused multi-omics integrative analysis. Since Yeast8, the yeast-GEM of Saccharomyces cerevisiae, published in 2019, has been continuously updated by the community. This has increased the quality and scope of the model, culminating now in Yeast9. To evaluate its predictive performance, we generated 163 condition-specific GEMs constrained by single-cell transcriptomics from osmotic pressure or reference conditions. Comparative flux analysis showed that yeast adapting to high osmotic pressure benefits from upregulating fluxes through central carbon metabolism. Furthermore, combining Yeast9 with proteomics revealed metabolic rewiring underlying its preference for nitrogen sources. Lastly, we created strain-specific GEMs (ssGEMs) constrained by transcriptomics for 1229 mutant strains. Well able to predict the strains' growth rates, fluxomics from those large-scale ssGEMs outperformed transcriptomics in predicting functional categories for all studied genes in machine learning models. Based on those findings we anticipate that Yeast9 will continue to empower systems biology studies of yeast metabolism.
Authors
- Hendrik G. Mengers (ORCID: https://orcid.org/0000-0002-5098-164X)
- Lars M. Blank (ORCID: https://orcid.org/0000-0003-0961-4976)
- Sebastián N. Mendoza (ORCID: https://orcid.org/0000-0002-2192-5569)
- Mihail Anton
- Albert Tafur Rangel (ORCID: https://orcid.org/0000-0002-9428-183X)
- Benjamín J. Sánchez (ORCID: https://orcid.org/0000-0001-6093-4110)
- Eduard J. Kerkhoven (ORCID: https://orcid.org/0000-0002-3593-5792)
- William T. Scott (ORCID: https://orcid.org/0000-0002-4029-2998)
- Hongzhong Lu (ORCID: https://orcid.org/0009-0005-8555-1841)
- Ulf W. Liebal (ORCID: https://orcid.org/0000-0001-5172-7339)
- JENS KVIST NIELSEN (ORCID: https://orcid.org/0000-0002-9955-6003)
- Cheng Wei Quan Eiden
- Lixin Zhang (ORCID: https://orcid.org/0000-0003-0894-9520)
- Chengyu Zhang (ORCID: https://orcid.org/0009-0004-3006-9073)
- Feiran Li (ORCID: https://orcid.org/0000-0001-9155-5260)
Institutions
- East China University of Science and Technology (CN)
- Nanyang Technological University (SG)
- Shanghai Jiao Tong University (CN)
- Science for Life Laboratory (SE)
- Novo Nordisk Foundation (DK)
- Tsinghua–Berkeley Shenzhen Institute (CN)
- BioInnovation Institute (DK)
- Chalmers University of Technology (SE)
- University of Chile (CL)
- Vrije Universiteit Amsterdam (NL)
- RWTH Aachen University (DE)
- Wageningen University & Research (NL)
- Technical University of Denmark (DK)
- Tsinghua University (CN)
Publication Details
- Journal
- Molecular Systems Biology
- Published
- 2024-08-12
- DOI
- https://doi.org/10.1038/s44320-024-00060-7
- Citations
- 38
- Primary Topic
- Microbial Metabolic Engineering and Bioproduction
- Type
- article
- Field-Weighted Citation Impact
- 8.89
Funders
- Institut Català de Nanociència i Nanotecnologia
- European Commission
- Deutsche Forschungsgemeinschaft
- National Natural Science Foundation of China
- Chalmers Tekniska Högskola
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek
- Knut och Alice Wallenbergs Stiftelse
- Novo Nordisk
- Consejo Nacional de Innovación, Ciencia y Tecnología
- Novo Nordisk Fonden
- Higher Education Discipline Innovation Project
- Agencia Nacional de Investigación y Desarrollo
- Horizon 2020 Framework Programme
- Comisión Nacional de Investigación Científica y Tecnológica
- National Key Research and Development Program of China
- Overseas Expertise Introduction Project for Discipline Innovation