The transcriptome and flux profiling of Crabtree-negative hydroxy acid producing strains of Saccharomyces cerevisiae reveals changes in the central carbon metabolism

Research output: Contribution to journalJournal article – Annual report year: 2019Researchpeer-review

Standard

Harvard

APA

CBE

MLA

Vancouver

Author

Bibtex

@article{ad99112686444edf88b2acb9dfe73436,
title = "The transcriptome and flux profiling of Crabtree-negative hydroxy acid producing strains of Saccharomyces cerevisiae reveals changes in the central carbon metabolism",
abstract = "Saccharomyces cerevisiae is a yeast cell factory of choice for the production of many bio-based chemicals. However, it is also a Crabtree-positive yeast and so it shuttles a large portion of carbon into ethanol, even under aerobic conditions. To minimise the carbon loss, ethanol formation can be eliminated by deleting pyruvate decarboxylase (PDC) activity. Deletion of PDC genes has a profound impact on S. cerevisiae physiology, and it is not yet well understood how PDC-negative yeasts are affected when engineered to produce other products than ethanol. In this study, we introduced pathways for the production of three hydroxy acids (lactic, malic, or 3-hydroxypropionic acid) into an evolved PDC-negative strain. We characterised these strains via transcriptome and flux profiling to elucidate the effects that the production of these hydroxy acids has on the host strain. The expression of lactic acid and malic acid biosynthesis pathways improved the maximum specific growth rate (μmax ) of the strain by 64 and 20{\%} respectively, presumably due to NAD+ regeneration. On the contrary, the 3HP pathways expression decreased the μmax . All strains showed a very high flux (>90{\%} of glucose uptake) into the oxidative pentose phosphate pathway under batch fermentation conditions. The transcriptional profile was least affected by the production of lactic acid and more by malic or 3-hydroxypropionic acids. The study, for the first time, directly compares the flux and transcriptome profiles of several different hydroxy acid producing strains of an evolved PDC-negative S. cerevisiae and suggests directions for future metabolic engineering. This article is protected by copyright. All rights reserved.",
keywords = "13C-based metabolic flux analysis, Crabtree-negative, Transcriptomics, central carbon metabolism, hydroxy acid",
author = "Jessop-Fabre, {Mathew M} and Jonathan Dahlin and Biron, {Mathias Bernfried} and Vratislav Stovicek and Ebert, {Birgitta E} and Blank, {Lars M} and Itay Budin and Keasling, {Jay D} and Irina Borodina",
year = "2019",
doi = "10.1002/biot.201900013",
language = "English",
journal = "Biotechnology Journal",
issn = "1860-6768",
publisher = "Wiley - V C H Verlag GmbH & Co. KGaA",

}

RIS

TY - JOUR

T1 - The transcriptome and flux profiling of Crabtree-negative hydroxy acid producing strains of Saccharomyces cerevisiae reveals changes in the central carbon metabolism

AU - Jessop-Fabre, Mathew M

AU - Dahlin, Jonathan

AU - Biron, Mathias Bernfried

AU - Stovicek, Vratislav

AU - Ebert, Birgitta E

AU - Blank, Lars M

AU - Budin, Itay

AU - Keasling, Jay D

AU - Borodina, Irina

PY - 2019

Y1 - 2019

N2 - Saccharomyces cerevisiae is a yeast cell factory of choice for the production of many bio-based chemicals. However, it is also a Crabtree-positive yeast and so it shuttles a large portion of carbon into ethanol, even under aerobic conditions. To minimise the carbon loss, ethanol formation can be eliminated by deleting pyruvate decarboxylase (PDC) activity. Deletion of PDC genes has a profound impact on S. cerevisiae physiology, and it is not yet well understood how PDC-negative yeasts are affected when engineered to produce other products than ethanol. In this study, we introduced pathways for the production of three hydroxy acids (lactic, malic, or 3-hydroxypropionic acid) into an evolved PDC-negative strain. We characterised these strains via transcriptome and flux profiling to elucidate the effects that the production of these hydroxy acids has on the host strain. The expression of lactic acid and malic acid biosynthesis pathways improved the maximum specific growth rate (μmax ) of the strain by 64 and 20% respectively, presumably due to NAD+ regeneration. On the contrary, the 3HP pathways expression decreased the μmax . All strains showed a very high flux (>90% of glucose uptake) into the oxidative pentose phosphate pathway under batch fermentation conditions. The transcriptional profile was least affected by the production of lactic acid and more by malic or 3-hydroxypropionic acids. The study, for the first time, directly compares the flux and transcriptome profiles of several different hydroxy acid producing strains of an evolved PDC-negative S. cerevisiae and suggests directions for future metabolic engineering. This article is protected by copyright. All rights reserved.

AB - Saccharomyces cerevisiae is a yeast cell factory of choice for the production of many bio-based chemicals. However, it is also a Crabtree-positive yeast and so it shuttles a large portion of carbon into ethanol, even under aerobic conditions. To minimise the carbon loss, ethanol formation can be eliminated by deleting pyruvate decarboxylase (PDC) activity. Deletion of PDC genes has a profound impact on S. cerevisiae physiology, and it is not yet well understood how PDC-negative yeasts are affected when engineered to produce other products than ethanol. In this study, we introduced pathways for the production of three hydroxy acids (lactic, malic, or 3-hydroxypropionic acid) into an evolved PDC-negative strain. We characterised these strains via transcriptome and flux profiling to elucidate the effects that the production of these hydroxy acids has on the host strain. The expression of lactic acid and malic acid biosynthesis pathways improved the maximum specific growth rate (μmax ) of the strain by 64 and 20% respectively, presumably due to NAD+ regeneration. On the contrary, the 3HP pathways expression decreased the μmax . All strains showed a very high flux (>90% of glucose uptake) into the oxidative pentose phosphate pathway under batch fermentation conditions. The transcriptional profile was least affected by the production of lactic acid and more by malic or 3-hydroxypropionic acids. The study, for the first time, directly compares the flux and transcriptome profiles of several different hydroxy acid producing strains of an evolved PDC-negative S. cerevisiae and suggests directions for future metabolic engineering. This article is protected by copyright. All rights reserved.

KW - 13C-based metabolic flux analysis

KW - Crabtree-negative

KW - Transcriptomics

KW - central carbon metabolism

KW - hydroxy acid

U2 - 10.1002/biot.201900013

DO - 10.1002/biot.201900013

M3 - Journal article

JO - Biotechnology Journal

JF - Biotechnology Journal

SN - 1860-6768

M1 - e1900013

ER -