Engineering cytosolic acetyl-CoA metabolism in Saccharomyces cerevisiae
Doktorsavhandling, 2015

A Saccharomyces cerevisiae strain carrying deletions in all three pyruvate decarboxylase genes (also called Pdc negative yeast) represents a non-ethanol producing platform strain for biochemical production. However, it cannot grow on glucose as the sole carbon source due to the lack of cytosolic acetyl-CoA for lipid biosynthesis. Its growth inability on glucose could be restored through directed evolution, which was explained by an in-frame internal deletion in MTH1 (MTH1-∆T). The MTH1-∆T allele resulted in reduced glucose uptake, which may attenuate the repression of respiratory metabolism. However, it was not clear what mechanism could provide the cells with sufficient precursors for cytosolic acetyl-CoA. Here we investigated this using a Pdc negative strain with MTH1-∆T, IMI076. Our results identified a route relying on Ach1 that could transfer acetyl units from mitochondria to the cytoplasm. Based on the results a new model was proposed, in which acetyl units are shuttled from the mitochondria to the cytoplasm in the form of acetate. In addition, a collection of Pdc negative strains was constructed and one of them was adaptively evolved on glucose via serial transfer. Three independently evolved strains were obtained, which can grow on glucose as the sole carbon source at maximum specific rates of 0.138 h-1, 0.148 h-1, 0.141 h-1, respectively. Several genetic changes were identified in the evolved Pdc negative strains by genome sequencing. Among these genetic changes, 4 genes were found to carry point mutations in at least two of the evolved strains: MTH1, HXT2, CIT1, and RPD3. Reverse engineering of the non-evolved Pdc negative strain through introduction of the MTH181D allele restored its growth on glucose at a maximum specific rate of 0.05 h-1 in minimal medium with 2% glucose. The non-synonymous mutations in HXT2 and CIT1 may function in the presence of mutated MTH1 alleles and could be related to an altered central carbon metabolism in order to ensure production of cytosolic acetyl-CoA in the Pdc negative strain. In connection with biobased chemical production, it is necessary to engineer the metabolism of cell factories such that the raw material, typically sugars, can be efficiently converted to the product of interest. Although IMI076 could grow on glucose, it was still inefficient at conversion of pyruvate to cytosolic acetyl-CoA. To increase cytosolic acetyl-CoA supply from pyruvate, pyruvate formate lyase and its activating enzyme from Escherichia coli were expressed with two different cofactors, ferredoxin or flavodoxin, and their reductase, respectively, and it was found that the co-expression of either of these cofactors had a positive effect on growth under aerobic conditions, indicating increased activity of PFL. The positive effect on growth was manifested as a higher final biomass concentration and a significant increase in transcription of formate dehydrogenase genes (FDHs). Among the two cofactors reduced flavodoxin was found to be a better electron donor than reduced ferredoxin.

reverse engineering


genomic DNA sequencing


histone deacetylase

adaptive evolution

ferredoxin/flavodoxin NADP+ reductase

pyruvate decarboxylase

citrate synthase

hexose transporter



aerobic growth

metabolic engineering.


central carbon metabolism

KC Lecture Hall
Opponent: Antonius J. A. van Maris


Yiming Zhang

Chalmers, Biologi och bioteknik, Systembiologi

With the requirements to provide fuels, chemicals and pharmaceuticals in sustainable ways, there is increasing focus in developing platform strains of yeast that can be used for production of a whole range of different products. Traditionally adaptive laboratory evolution is used in strain development through classical strain engineering based on mutagenesis and screening, an efficient approach for many different chemicals. The development of metabolic engineering offers tremendous opportunities to develop tailor made cell factories for efficient production of fuels and chemicals. Recently, impressive progresses achieved in systems biology and bioinformatics allow for rapid, affordable, high throughput techniques accessible for genome analysis. The identified genetic changes in adaptively evolved strains can be immediately and exactly reconstructed in native strains using ‘reverse’ metabolic engineering, to identify those responsible for the changes in phenotypes, which will elucidate underlying mechanisms for improved performance of adaptively evolved strains. In this thesis, metabolic engineering and adaptive laboratory evolution were combined to develop a non-ethanol producing platform strain of S. cerevisiae as a cell factory to convert glucose to cytosolic acetyl-CoA for biochemical production. Our findings will be useful for the fundamental understanding of acetyl-CoA metabolism in yeast, as well as strain development for biochemical production as cell factories.


Hållbar utveckling

Innovation och entreprenörskap




Livsvetenskaper och teknik (2010-2018)



KC Lecture Hall

Opponent: Antonius J. A. van Maris

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