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

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

doi:10.1016/j.ymben.2018.08.006

Cited by 17 publications

(7 citation statements)

References 72 publications

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“…5). Previous study found that S. cerevisiae responded to increasing NADPH requirement by the upregulation of genes in the oxidative PP pathway [45, 46]. The downregulation of these two genes during the HJ06P/HJ06 and HJ06PN/HJ06 comparisons was in agreement with the flux change (Figs.…”

Section: Discussionsupporting

confidence: 82%

13C metabolic flux analysis-guided metabolic engineering of Escherichia coli for improved acetol production from glycerol

Yao

Feng

et al. 2019

Biotechnol Biofuels

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BackgroundBioprocessing offers a sustainable and green approach to manufacture various chemicals and materials. Development of bioprocesses requires transforming common producer strains to cell factories. 13C metabolic flux analysis (13C-MFA) can be applied to identify relevant targets to accomplish the desired phenotype, which has become one of the major tools to support systems metabolic engineering. In this research, we applied 13C-MFA to identify bottlenecks in the bioconversion of glycerol into acetol by Escherichia coli. Valorization of glycerol, the main by-product of biodiesel, has contributed to the viability of biofuel economy.ResultsWe performed 13C-MFA and measured intracellular pyridine nucleotide pools in a first-generation acetol producer strain (HJ06) and a non-producer strain (HJ06C), and identified that engineering the NADPH regeneration is a promising target. Based on this finding, we overexpressed nadK encoding NAD kinase or pntAB encoding membrane-bound transhydrogenase either individually or in combination with HJ06, obtaining HJ06N, HJ06P and HJ06PN. The step-wise approach resulted in increasing the acetol titer from 0.91 g/L (HJ06) to 2.81 g/L (HJ06PN). To systematically characterize and the effect of mutation(s) on the metabolism, we also examined the metabolomics and transcriptional levels of key genes in four strains. The pool sizes of NADPH, NADP+ and the NADPH/NADP+ ratio were progressively increased from HJ06 to HJ06PN, demonstrating that the sufficient NADPH supply is critical for acetol production. Flux distribution was optimized towards acetol formation from HJ06 to HJ06PN: (1) The carbon partitioning at the DHAP node directed gradually more carbon from the lower glycolytic pathway through the acetol biosynthetic pathway; (2) The transhydrogenation flux was constantly increased. In addition, 13C-MFA showed the rigidity of upper glycolytic pathway, PP pathway and the TCA cycle to support growth. The flux patterns were supported by most metabolomics data and gene expression profiles.ConclusionsThis research demonstrated how 13C-MFA can be applied to drive the cycles of design, build, test and learn implementation for strain development. This succeeding engineering strategy can also be applicable for rational design of other microbial cell factories.Electronic supplementary materialThe online version of this article (10.1186/s13068-019-1372-4) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 82%

13C metabolic flux analysis-guided metabolic engineering of Escherichia coli for improved acetol production from glycerol

Yao

Feng

et al. 2019

Biotechnol Biofuels

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“…Recently, systemic ‘omics approaches proved to be useful in identifying specific genetic targets of modification by providing an integrated view of cell physiology, firstly describing wine yeast metabolism in detail, to understand the complex regulatory networks that occur in this organism during wine fermentation [ 46 ].…”

Section: Metabolic Regulation In Ethanol Reduction Using Coculturementioning

confidence: 99%

Yeast Interactions and Molecular Mechanisms in Wine Fermentation: A Comprehensive Review

Comitini

Agarbati

Canonico

2021

IJMS

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Wine can be defined as a complex microbial ecosystem, where different microorganisms interact in the function of different biotic and abiotic factors. During natural fermentation, the effect of unpredictable interactions between microorganisms and environmental factors leads to the establishment of a complex and stable microbiota that will define the kinetics of the process and the final product. Controlled multistarter fermentation represents a microbial approach to achieve the dual purpose of having a less risky process and a distinctive final product. Indeed, the interactions evolved between microbial consortium members strongly modulate the final sensorial properties of the wine. Therefore, in well-managed mixed fermentations, the knowledge of molecular mechanisms on the basis of yeast interactions, in a well-defined ecological niche, becomes fundamental to control the winemaking process, representing a tool to achieve such objectives. In the present work, the recent development on the molecular and metabolic interactions between non-Saccharomyces and Saccharomyces yeasts in wine fermentation was reviewed. A particular focus will be reserved on molecular studies regarding the role of nutrients, the production of the main byproducts and volatile compounds, ethanol reduction, and antagonistic actions for biological control in mixed fermentations.

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“…PDC5 was among genes induced along DC5 in fermentations associated with H. uvarum ( Table S2 ). PDC5 encodes one of three isoforms of pyruvate decarboxylase, an enzyme involved in the formation of flavor-active higher alcohols in wine via the Ehrlich pathway ( 48 – 50 ). In wine fermentations, overexpression of PDC5 has led to increased concentrations of 2,3-butanediol, other higher alcohols, and acetaldehyde ( 46 , 49 , 50 ).…”

Section: Resultsmentioning

confidence: 99%

“…PDC5 encodes one of three isoforms of pyruvate decarboxylase, an enzyme involved in the formation of flavor-active higher alcohols in wine via the Ehrlich pathway ( 48 – 50 ). In wine fermentations, overexpression of PDC5 has led to increased concentrations of 2,3-butanediol, other higher alcohols, and acetaldehyde ( 46 , 49 , 50 ). This suggests that the presence of H. uvarum may lead to gene expression changes directly impacting wine sensory outcomes.…”

Section: Resultsmentioning

confidence: 99%

Charting Shifts in Saccharomyces cerevisiae Gene Expression across Asynchronous Time Trajectories with Diffusion Maps

Reiter

Montpetit

Runnebaum

et al. 2021

mBio

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

Cited by 17 publications

References 72 publications

13C metabolic flux analysis-guided metabolic engineering of Escherichia coli for improved acetol production from glycerol

13C metabolic flux analysis-guided metabolic engineering of Escherichia coli for improved acetol production from glycerol

Yeast Interactions and Molecular Mechanisms in Wine Fermentation: A Comprehensive Review

Charting Shifts in Saccharomyces cerevisiae Gene Expression across Asynchronous Time Trajectories with Diffusion Maps

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