Genome-scale modeling drives 70-fold improvement of intracellular heme production in Saccharomyces cerevisiae
Journal article, 2022

Heme is an oxygen carrier and a cofactor of both industrial enzymes and food additives. The intracellular level of free heme is low, which limits the synthesis of heme proteins. Therefore, increasing heme synthesis allows an increased production of heme proteins. Using the genome-scale metabolic model (GEM) Yeast8 for the yeast Saccharomyces cerevisiae, we identified fluxes potentially important to heme synthesis. With this model, in silico simulations highlighted 84 gene targets for balancing biomass and increasing heme production. Of those identified, 76 genes were individually deleted or overexpressed in experiments. Empirically, 40 genes individually increased heme production (up to threefold). Heme was increased by modifying target genes, which not only included the genes involved in heme biosynthesis, but also those involved in glycolysis, pyruvate, Fe-S clusters, glycine, and succinyl-coenzyme A (CoA) metabolism. Next, we developed an algorithmic method for predicting an optimal combination of these genes by using the enzyme-constrained extension of the Yeast8 model, ecYeast8. The computationally identified combination for enhanced heme production was evaluated using the heme ligand-binding biosensor (Heme-LBB). The positive targets were combined using CRISPR-Cas9 in the yeast strain (IMX581-HEM15-HEM14-HEM3- δshm1-HEM2-δhmx1-FET4-δgcv2-HEM1-δgcv1-HEM13), which produces 70-foldhigher levels of intracellular heme.

Genome-scale modeling

heme ligand-binding biosensor

metabolic engineering

heme

Saccharomyces cerevisiae

Author

Olena Ishchuk

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Iván Domenzain Del Castillo Cerecer

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Novo Nordisk Foundation

Benjamín José Sánchez

Technical University of Denmark (DTU)

Novo Nordisk Foundation

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Facundo Muniz

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Jose Luis Martinez Ruiz

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Technical University of Denmark (DTU)

Jens B Nielsen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

BioInnovation Institute

Novo Nordisk Foundation

Dina Petranovic Nielsen

Novo Nordisk Foundation

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Proceedings of the National Academy of Sciences of the United States of America

0027-8424 (ISSN) 1091-6490 (eISSN)

Vol. 119 30 e2108245119

Subject Categories

Biochemistry and Molecular Biology

Bioinformatics and Systems Biology

Biocatalysis and Enzyme Technology

DOI

10.1073/pnas.2108245119

PubMed

35858410

More information

Latest update

5/26/2023