Rewiring regulation on respiro-fermentative metabolism relieved Crabtree effects in Saccharomyces cerevisiae

Zhang, Yiming; Su, Mo; Wang, Zheng; Nielsen, Jens; Liu, Zihe

doi:10.1016/j.synbio.2022.06.004

Cited by 11 publications

(4 citation statements)

References 53 publications

(75 reference statements)

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“…In S. cerevisiae , the Crabtree effect, which is the balance between fermentation and respiration metabolism, is driven by differential regulation levels of hypoxia genes and genes involved in oxidative phosphorylation in mitochondria. [ 50 ] Compared with S288C, the weaker Crabtree effect of WY319 might be achieved by enhancing the inhibition of hypoxia genes and boosting mitochondrial responsiveness, thereby shifting to a metabolic mode with a higher respiration/fermentation ratio, which is beneficial for 2‐PE production and stress response to product. This regulation might pivot on alterations in some sequences of the aforementioned transcription factors, and related molecular validation experiments for these specific targets are currently underway.…”

Section: Resultsmentioning

confidence: 99%

Unveiling the mechanism of efficient β‐phenylethyl alcohol conversion in wild‐type Saccharomyces cerevisiae WY319 through multi‐omics analysis

Yang,

Ren,

et al. 2024

Biotechnology Journal

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Abstractβ‐Phenylethanol (2‐PE), as an important flavor component in wine, is widely used in the fields of flavor chemistry and food health. 2‐PE can be sustainably produced through Saccharomyces cerevisiae. Although significant progress has been made in obtaining high‐yield strains, as well as improving the synthesis pathways of 2‐PE, there still lies a gap between these two fields to unpin. In this study, the macroscopic metabolic characteristics of high‐yield and low‐yield 2‐PE strains were systematically compared and analyzed. The results indicated that the production potential of the high‐yield strain might be contributed to the enhancement of respiratory metabolism and the high tolerance to 2‐PE. Furthermore, this hypothesis was confirmed through comparative genomics. Meanwhile, transcriptome analysis at key specific growth rates revealed that the collective upregulation of mitochondrial functional gene clusters plays a more prominent role in the production process of 2‐PE. Finally, findings from untargeted metabolomics suggested that by enhancing respiratory metabolism and reducing the Crabtree effect, the accumulation of metabolites resisting high 2‐PE stress was observed, such as intracellular amino acids and purines. Hence, this strategy provided a richer supply of precursors and cofactors, effectively promoting the synthesis of 2‐PE. In short, this study provides a bridge for studying the metabolic mechanism of high‐yield 2‐PE strains with the subsequent targeted strengthening of relevant synthetic pathways. It also provides insights for the synthesis of nonalcoholic products in S. cerevisiae.

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Section: Resultsmentioning

confidence: 99%

Unveiling the mechanism of efficient β‐phenylethyl alcohol conversion in wild‐type Saccharomyces cerevisiae WY319 through multi‐omics analysis

Yang,

Ren,

et al. 2024

Biotechnology Journal

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“…In our previous research, we noticed that when the mitochondrial MCR was expressed in an episomal plasmid, the 3-HP titer reached 0.27 g/L [ 39 ], compared to the titer of 0.09 g/L when the cytosolic MCR was expressed [ 21 ], suggesting the yeast mitochondrion as an attractive subcellular compartment for 3-HP synthesis. With mitochondrial CaMCR integrated into the XI-3 site of the chromosome, the strain mMCR1 produced 0.11 g/L 3-HP, suggesting that CaMCR activity was crucial for 3-HP production.…”

Section: Resultsmentioning

confidence: 99%

“…The intact MCR from Chloroflexus aurantiacus was cloned in pMCR1, while its dissected parts of MCR-N and MCR-C were cloned in pMCR2 in a previous study for mitochondrial localization [ 39 ]. The plasmid pMCR-mC was constructed to introduce the mutations N940V, K1106W, and S1114R into MCR-C by assembling 3 fragments amplified with primers MP1–4 from pMCR2 [ 39 ] into the vector pUGG1. The plasmid pMCR3 was constructed by assembling the fragments of MCR-N amplified with primers MP5&6 and MCR-mC amplified with primers MP7&8 into pUGG1.…”

Section: Methodsmentioning

confidence: 99%

Engineering yeast mitochondrial metabolism for 3-hydroxypropionate production

Zhang

Chen

et al. 2023

Biotechnol Biofuels

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Background With unique physiochemical environments in subcellular organelles, there has been growing interest in harnessing yeast organelles for bioproduct synthesis. Among these organelles, the yeast mitochondrion has been found to be an attractive compartment for production of terpenoids and branched-chain alcohols, which could be credited to the abundant supply of acetyl-CoA, ATP and cofactors. In this study we explored the mitochondrial potential for production of 3-hydroxypropionate (3-HP) and performed the cofactor engineering and flux control at the acetyl-CoA node to maximize 3-HP synthesis. Results Metabolic modeling suggested that the mitochondrion serves as a more suitable compartment for 3-HP synthesis via the malonyl-CoA pathway than the cytosol, due to the opportunity to obtain a higher maximum yield and a lower oxygen consumption. With the malonyl-CoA reductase (MCR) targeted into the mitochondria, the 3-HP production increased to 0.27 g/L compared with 0.09 g/L with MCR expressed in the cytosol. With enhanced expression of dissected MCR enzymes, the titer reached to 4.42 g/L, comparable to the highest titer achieved in the cytosol so far. Then, the mitochondrial NADPH supply was optimized by overexpressing POS5 and IDP1, which resulted in an increase in the 3-HP titer to 5.11 g/L. Furthermore, with induced expression of an ACC1 mutant in the mitochondria, the final 3-HP production reached 6.16 g/L in shake flask fermentations. The constructed strain was then evaluated in fed-batch fermentations, and produced 71.09 g/L 3-HP with a productivity of 0.71 g/L/h and a yield on glucose of 0.23 g/g. Conclusions In this study, the yeast mitochondrion is reported as an attractive compartment for 3-HP production. The final 3-HP titer of 71.09 g/L with a productivity of 0.71 g/L/h was achieved in fed-batch fermentations, representing the highest titer reported for Saccharomyces cerevisiae so far, that demonstrated the potential of recruiting the yeast mitochondria for further development of cell factories.

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“…This Crabtree effect is a consequence of high rates of sugar uptake and increased glycolytic fluxes, and due to a limited respiratory capacity results in overflow metabolism and ethanol production [68]. In order to increase respiration and cell biomass by this yeast, two main approaches were developed: reducing or restricting sugar uptake to prevent carbon overflow to ethanol [69][70][71], or interfering in the transcriptional control of metabolism [72][73][74][75][76]. In line with the importance of gene regulation for the establishment of the Crabtree effect is a report showing that overexpression of a single transcriptional regulator of the zinc cluster family (encoded by the CRA1 gene) transforms the typical Crabtree-negative yeast K. phaffii into a Crabtreepositive yeast that produces ethanol under aerobic conditions [77].…”

Section: The Precision Fermentation Processmentioning

confidence: 99%

Precision Fermentation as an Alternative to Animal Protein, a Review

Knychala,

Boing,

Ienczak

et al. 2024

Fermentation

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The global food production system faces several challenges, including significant environmental impacts due to traditional agricultural practices. The rising demands of consumers for food products that are safe, healthy, and have animal welfare standards have led to an increased interest in alternative proteins and the development of the cellular agriculture field. Within this innovative field, precision fermentation has emerged as a promising technological solution to produce proteins with reduced ecological footprints. This review provides a summary of the environmental impacts related to the current global food production, and explores how precision fermentation can contribute to address these issues. Additionally, we report on the main animal-derived proteins produced by precision fermentation, with a particular focus on those used in the food and nutraceutical industries. The general principles of precision fermentation will be explained, including strain and bioprocess optimization. Examples of efficient recombinant protein production by bacteria and yeasts, such as milk proteins, egg-white proteins, structural and flavoring proteins, will also be addressed, along with case examples of companies producing these recombinant proteins at a commercial scale. Through these examples, we explore how precision fermentation supports sustainable food production and holds the potential for significant innovations in the sector.

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Rewiring regulation on respiro-fermentative metabolism relieved Crabtree effects in Saccharomyces cerevisiae

Cited by 11 publications

References 53 publications

Unveiling the mechanism of efficient β‐phenylethyl alcohol conversion in wild‐type Saccharomyces cerevisiae WY319 through multi‐omics analysis

Unveiling the mechanism of efficient β‐phenylethyl alcohol conversion in wild‐type Saccharomyces cerevisiae WY319 through multi‐omics analysis

Engineering yeast mitochondrial metabolism for 3-hydroxypropionate production

Precision Fermentation as an Alternative to Animal Protein, a Review

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