Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains

Cristian Varela, Simon A. Schmidt, Anthony R. Borneman, Chi Nam Ignatius Pang, Jens O. Krömerx, Alamgir Khan, Xiaomin Song, Mark P. Hodson, Mark Solomon, Christine M. Mayr, Wade Hines, Isak S. Pretorius, Mark S. Baker, Ute Roessner, Meagan Mercurio, Paul A. Henschke, Marc R. Wilkins, Paul J. Chambers

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Metabolic engineering has been vital to the development of industrial microbes such as the yeast Saccharomyces cerevisiae. However, sequential rounds of modification are often needed to achieve particular industrial design targets. Systems biology approaches can aid in identifying genetic targets for modification through providing an integrated view of cellular physiology. Recently, research into the generation of commercial yeasts that can produce reduced-ethanol wines has resulted in metabolically-engineered strains of S. cerevisiae that are less efficient at producing ethanol from sugar. However, these modifications led to the concomitant production of off-flavour by-products. A combination of transcriptomics, proteomics and metabolomics was therefore used to investigate the physiological changes occurring in an engineered low-ethanol yeast strain during alcoholic fermentation. Integration of ‘omics data identified several metabolic reactions, including those related to the pyruvate node and redox homeostasis, as being significantly affected by the low-ethanol engineering methodology, and highlighted acetaldehyde and 2,4,5-trimethyl-1,3-dioxolane as the main off-flavour compounds. Gene remediation strategies were then successfully applied to decrease the formation of these by-products, while maintaining the ‘low-alcohol’ phenotype. The data generated from this comprehensive systems-based study will inform wine yeast strain development programmes, which, in turn, could potentially play an important role in assisting winemakers in their endeavour to produce low-alcohol wines with desirable flavour profiles.

LanguageEnglish
Pages178-191
Number of pages14
JournalMetabolic Engineering
Volume49
DOIs
Publication statusPublished - 1 Sep 2018

Fingerprint

Wine
Flavors
Yeast
Ethanol
Genes
Yeasts
Saccharomyces cerevisiae
Alcohols
Metabolic Engineering
Metabolomics
Systems Biology
Byproducts
Acetaldehyde
Flavor compounds
Pyruvic Acid
Proteomics
Metabolic engineering
Fermentation
Oxidation-Reduction
Homeostasis

Keywords

  • Low-alcohol
  • Systems biology
  • Wine
  • Yeast

Cite this

Varela, Cristian ; Schmidt, Simon A. ; Borneman, Anthony R. ; Pang, Chi Nam Ignatius ; Krömerx, Jens O. ; Khan, Alamgir ; Song, Xiaomin ; Hodson, Mark P. ; Solomon, Mark ; Mayr, Christine M. ; Hines, Wade ; Pretorius, Isak S. ; Baker, Mark S. ; Roessner, Ute ; Mercurio, Meagan ; Henschke, Paul A. ; Wilkins, Marc R. ; Chambers, Paul J. / Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains. In: Metabolic Engineering. 2018 ; Vol. 49. pp. 178-191.
@article{ceb3d203ea9446659bab1ac5ce313469,
title = "Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains",
abstract = "Metabolic engineering has been vital to the development of industrial microbes such as the yeast Saccharomyces cerevisiae. However, sequential rounds of modification are often needed to achieve particular industrial design targets. Systems biology approaches can aid in identifying genetic targets for modification through providing an integrated view of cellular physiology. Recently, research into the generation of commercial yeasts that can produce reduced-ethanol wines has resulted in metabolically-engineered strains of S. cerevisiae that are less efficient at producing ethanol from sugar. However, these modifications led to the concomitant production of off-flavour by-products. A combination of transcriptomics, proteomics and metabolomics was therefore used to investigate the physiological changes occurring in an engineered low-ethanol yeast strain during alcoholic fermentation. Integration of ‘omics data identified several metabolic reactions, including those related to the pyruvate node and redox homeostasis, as being significantly affected by the low-ethanol engineering methodology, and highlighted acetaldehyde and 2,4,5-trimethyl-1,3-dioxolane as the main off-flavour compounds. Gene remediation strategies were then successfully applied to decrease the formation of these by-products, while maintaining the ‘low-alcohol’ phenotype. The data generated from this comprehensive systems-based study will inform wine yeast strain development programmes, which, in turn, could potentially play an important role in assisting winemakers in their endeavour to produce low-alcohol wines with desirable flavour profiles.",
keywords = "Low-alcohol, Systems biology, Wine, Yeast",
author = "Cristian Varela and Schmidt, {Simon A.} and Borneman, {Anthony R.} and Pang, {Chi Nam Ignatius} and Kr{\"o}merx, {Jens O.} and Alamgir Khan and Xiaomin Song and Hodson, {Mark P.} and Mark Solomon and Mayr, {Christine M.} and Wade Hines and Pretorius, {Isak S.} and Baker, {Mark S.} and Ute Roessner and Meagan Mercurio and Henschke, {Paul A.} and Wilkins, {Marc R.} and Chambers, {Paul J.}",
year = "2018",
month = "9",
day = "1",
doi = "10.1016/j.ymben.2018.08.006",
language = "English",
volume = "49",
pages = "178--191",
journal = "Metabolic Engineering",
issn = "1096-7176",
publisher = "Academic Press Inc.",

}

Varela, C, Schmidt, SA, Borneman, AR, Pang, CNI, Krömerx, JO, Khan, A, Song, X, Hodson, MP, Solomon, M, Mayr, CM, Hines, W, Pretorius, IS, Baker, MS, Roessner, U, Mercurio, M, Henschke, PA, Wilkins, MR & Chambers, PJ 2018, 'Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains' Metabolic Engineering, vol. 49, pp. 178-191. https://doi.org/10.1016/j.ymben.2018.08.006

Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains. / Varela, Cristian; Schmidt, Simon A.; Borneman, Anthony R.; Pang, Chi Nam Ignatius; Krömerx, Jens O.; Khan, Alamgir; Song, Xiaomin; Hodson, Mark P.; Solomon, Mark; Mayr, Christine M.; Hines, Wade; Pretorius, Isak S.; Baker, Mark S.; Roessner, Ute; Mercurio, Meagan; Henschke, Paul A.; Wilkins, Marc R.; Chambers, Paul J.

In: Metabolic Engineering, Vol. 49, 01.09.2018, p. 178-191.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains

AU - Varela,Cristian

AU - Schmidt,Simon A.

AU - Borneman,Anthony R.

AU - Pang,Chi Nam Ignatius

AU - Krömerx,Jens O.

AU - Khan,Alamgir

AU - Song,Xiaomin

AU - Hodson,Mark P.

AU - Solomon,Mark

AU - Mayr,Christine M.

AU - Hines,Wade

AU - Pretorius,Isak S.

AU - Baker,Mark S.

AU - Roessner,Ute

AU - Mercurio,Meagan

AU - Henschke,Paul A.

AU - Wilkins,Marc R.

AU - Chambers,Paul J.

PY - 2018/9/1

Y1 - 2018/9/1

N2 - Metabolic engineering has been vital to the development of industrial microbes such as the yeast Saccharomyces cerevisiae. However, sequential rounds of modification are often needed to achieve particular industrial design targets. Systems biology approaches can aid in identifying genetic targets for modification through providing an integrated view of cellular physiology. Recently, research into the generation of commercial yeasts that can produce reduced-ethanol wines has resulted in metabolically-engineered strains of S. cerevisiae that are less efficient at producing ethanol from sugar. However, these modifications led to the concomitant production of off-flavour by-products. A combination of transcriptomics, proteomics and metabolomics was therefore used to investigate the physiological changes occurring in an engineered low-ethanol yeast strain during alcoholic fermentation. Integration of ‘omics data identified several metabolic reactions, including those related to the pyruvate node and redox homeostasis, as being significantly affected by the low-ethanol engineering methodology, and highlighted acetaldehyde and 2,4,5-trimethyl-1,3-dioxolane as the main off-flavour compounds. Gene remediation strategies were then successfully applied to decrease the formation of these by-products, while maintaining the ‘low-alcohol’ phenotype. The data generated from this comprehensive systems-based study will inform wine yeast strain development programmes, which, in turn, could potentially play an important role in assisting winemakers in their endeavour to produce low-alcohol wines with desirable flavour profiles.

AB - Metabolic engineering has been vital to the development of industrial microbes such as the yeast Saccharomyces cerevisiae. However, sequential rounds of modification are often needed to achieve particular industrial design targets. Systems biology approaches can aid in identifying genetic targets for modification through providing an integrated view of cellular physiology. Recently, research into the generation of commercial yeasts that can produce reduced-ethanol wines has resulted in metabolically-engineered strains of S. cerevisiae that are less efficient at producing ethanol from sugar. However, these modifications led to the concomitant production of off-flavour by-products. A combination of transcriptomics, proteomics and metabolomics was therefore used to investigate the physiological changes occurring in an engineered low-ethanol yeast strain during alcoholic fermentation. Integration of ‘omics data identified several metabolic reactions, including those related to the pyruvate node and redox homeostasis, as being significantly affected by the low-ethanol engineering methodology, and highlighted acetaldehyde and 2,4,5-trimethyl-1,3-dioxolane as the main off-flavour compounds. Gene remediation strategies were then successfully applied to decrease the formation of these by-products, while maintaining the ‘low-alcohol’ phenotype. The data generated from this comprehensive systems-based study will inform wine yeast strain development programmes, which, in turn, could potentially play an important role in assisting winemakers in their endeavour to produce low-alcohol wines with desirable flavour profiles.

KW - Low-alcohol

KW - Systems biology

KW - Wine

KW - Yeast

UR - http://www.scopus.com/inward/record.url?scp=85052093111&partnerID=8YFLogxK

U2 - 10.1016/j.ymben.2018.08.006

DO - 10.1016/j.ymben.2018.08.006

M3 - Article

VL - 49

SP - 178

EP - 191

JO - Metabolic Engineering

T2 - Metabolic Engineering

JF - Metabolic Engineering

SN - 1096-7176

ER -