Advances in genome-scale metabolic models of industrially important fungi
Review article, 2023

Many fungal species have been used industrially for production of biofuels and bioproducts. Developing strains with better performance in biomanufacturing contexts requires a systematic understanding of cellular metabolism. Genome-scale metabolic models (GEMs) offer a comprehensive view of interconnected pathways and a mathematical framework for downstream analysis. Recently, GEMs have been developed or updated for several industrially important fungi. Some of them incorporate enzyme constraints, enabling improved predictions of cell states and proteome allocation. Here, we provide an overview of these newly developed GEMs and computational methods that facilitate construction of enzyme-constrained GEMs and utilize flux predictions from GEMs. Furthermore, we highlight the pivotal roles of these GEMs in iterative design–build–test–learn cycles, ultimately advancing the field of fungal biomanufacturing.

Genome-scale metabolic models

Author

Yichao Han

Pacific Northwest National Laboratory

Albert Enrique Tafur Rangel

Chalmers, Life Sciences, Systems and Synthetic Biology

Novo Nordisk Foundation

Kyle R. Pomraning

Pacific Northwest National Laboratory

Eduard Kerkhoven

Science for Life Laboratory (SciLifeLab)

Novo Nordisk Foundation

Chalmers, Life Sciences, Systems and Synthetic Biology

Joonhoon Kim

Pacific Northwest National Laboratory

United States Department of Energy

Current Opinion in Biotechnology

0958-1669 (ISSN) 1879-0429 (eISSN)

Vol. 84 103005

Subject Categories

Bioinformatics (Computational Biology)

Software Engineering

Bioinformatics and Systems Biology

DOI

10.1016/j.copbio.2023.103005

PubMed

37797483

More information

Latest update

10/16/2023