scholarly journals Curation and Analysis of a Saccharomyces cerevisiae Genome-Scale Metabolic Model for Predicting Production of Sensory Impact Molecules under Enological Conditions

Processes ◽  
2020 ◽  
Vol 8 (9) ◽  
pp. 1195
Author(s):  
William T. Scott ◽  
Eddy J. Smid ◽  
Richard A. Notebaart ◽  
David E. Block
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Alcoholic Fermentation ◽  
Sulfur Metabolism ◽  
Metabolic Model ◽  
Growth Conditions ◽  
Ehrlich Pathway ◽  
Flux Variability Analysis ◽  
Ester Formation ◽  
Genome Scale ◽  
New Strategies

One approach for elucidating strain-to-strain metabolic differences is the use of genome-scale metabolic models (GSMMs). To date GSMMs have not focused on the industrially important area of flavor production and, as such; do not cover all the pathways relevant to flavor formation in yeast. Moreover, current models for Saccharomyces cerevisiae generally focus on carbon-limited and/or aerobic systems, which is not pertinent to enological conditions. Here, we curate a GSMM (iWS902) to expand on the existing Ehrlich pathway and ester formation pathways central to aroma formation in industrial winemaking, in addition to the existing sulfur metabolism and medium-chain fatty acid (MCFA) pathways that also contribute to production of sensory impact molecules. After validating the model using experimental data, we predict key differences in metabolism for a strain (EC 1118) in two distinct growth conditions, including differences for aroma impact molecules such as acetic acid, tryptophol, and hydrogen sulfide. Additionally, we propose novel targets for metabolic engineering for aroma profile modifications employing flux variability analysis with the expanded GSMM. The model provides mechanistic insights into the key metabolic pathways underlying aroma formation during alcoholic fermentation and provides a potential framework to contribute to new strategies to optimize the aroma of wines.

scholarly journals The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

2008 ◽  
Vol 2 (1) ◽  
pp. 71 ◽  
Author(s):  
Intawat Nookaew ◽  
Michael C Jewett ◽  
Asawin Meechai ◽  
Chinae Thammarongtham ◽  
Kobkul Laoteng ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Lipid Metabolism ◽  
Metabolic Model ◽  
Genome Scale

scholarly journals Exposure of Saccharomyces cerevisiae to Acetaldehyde Induces Sulfur Amino Acid Metabolism and Polyamine Transporter Genes, Which Depend on Met4p and Haa1p Transcription Factors, Respectively

2004 ◽  
Vol 70 (4) ◽  
pp. 1913-1922 ◽  
Author(s):  
Agustín Aranda ◽  
Marcel-lí del Olmo
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Biosynthesis ◽  
Sulfur Metabolism ◽  
Cell Cycle Control ◽  
Control Cell ◽  
Mitochondrial Protein ◽  
Vitamin B1 ◽  
Global Gene Expression ◽  
Growth Conditions ◽  
Yeast Cells

ABSTRACT Acetaldehyde is a toxic compound produced by Saccharomyces cerevisiae cells under several growth conditions. The adverse effects of this molecule are important, as significant amounts accumulate inside the cells. By means of global gene expression analyses, we have detected the effects of acetaldehyde addition in the expression of about 400 genes. Repressed genes include many genes involved in cell cycle control, cell polarity, and the mitochondrial protein biosynthesis machinery. Increased expression is displayed in many stress response genes, as well as other families of genes, such as those encoding vitamin B1 biosynthesis machinery and proteins for aryl alcohol metabolism. The induction of genes involved in sulfur metabolism is dependent on Met4p and other well-known factors involved in the transcription of MET genes under nonrepressing conditions of sulfur metabolism. Moreover, the deletion of MET4 leads to increased acetaldehyde sensitivity. TPO genes encoding polyamine transporters are also induced by acetaldehyde; in this case, the regulation is dependent on the Haa1p transcription factor. In this paper, we discuss the connections between acetaldehyde and the processes affected by this compound in yeast cells with reference to the microarray data.

scholarly journals An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction

Metabolites ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 84 ◽  
Author(s):  
Amornpan Klanchui ◽  
Sudarat Dulsawat ◽  
Kullapat Chaloemngam ◽  
Supapon Cheevadhanarak ◽  
Peerada Prommeenate ◽  
...  
Keyword(s):  
Predictive Model ◽  
Metabolic Model ◽  
Arthrospira Platensis ◽  
Growth Conditions ◽  
Bioethanol Production ◽  
Cellular Behavior ◽  
Nutrient Limitations ◽  
A Genome ◽  
Simulation Results ◽  
Genome Scale

Glycogen-enriched biomass of Arthrospira platensis has increasingly gained attention as a source for bioethanol production. To study the metabolic capabilities of glycogen production in A. platensis C1, a genome-scale metabolic model (GEM) could be a useful tool for predicting cellular behavior and suggesting strategies for glycogen overproduction. New experimentally validated GEM of A. platensis C1 namely iAK888, which has improved metabolic coverage and functionality was employed in this research. The iAK888 is a fully functional compartmentalized GEM consisting of 888 genes, 1,096 reactions, and 994 metabolites. This model was demonstrated to reasonably predict growth and glycogen fluxes under different growth conditions. In addition, iAK888 was further employed to predict the effect of deficiencies of NO3−, PO43−, or SO42− on the growth and glycogen production in A. platensis C1. The simulation results showed that these nutrient limitations led to a decrease in growth flux and an increase in glycogen flux. The experiment of A. platensis C1 confirmed the enhancement of glycogen fluxes after the cells being transferred from normal Zarrouk’s medium to either NO3−, PO43−, or SO42−-free Zarrouk’s media. Therefore, iAK888 could be served as a predictive model for glycogen overproduction and a valuable multidisciplinary tool for further studies of this important academic and industrial organism.

scholarly journals Genome-scale metabolic model of the diatom Thalassiosira pseudonana highlights the importance of nitrogen and sulfur metabolism in redox balance

2020 ◽  
Author(s):  
Helena M. van Tol ◽  
E. Virginia Armbrust
Keyword(s):  
Organic Matter ◽  
Sulfur Metabolism ◽  
Reducing Power ◽  
Metabolic Model ◽  
Redox Balance ◽  
Thalassiosira Pseudonana ◽  
Cellular Damage ◽  
Marine Microorganisms ◽  
A Genome ◽  
Genome Scale

AbstractDiatoms are unicellular photosynthetic algae known to secrete organic matter that fuels secondary production in the ocean, though our knowledge of how their physiology impacts the character of dissolved organic matter remains limited. Like all photosynthetic organisms, their use of light for energy and reducing power creates the challenge of avoiding cellular damage. To better understand the interplay between redox balance and organic matter secretion, we reconstructed a genome-scale metabolic model of Thalassiosira pseudonana strain CCMP 1335, a model for diatom molecular biology and physiology, with a 60-year history of studies. The model simulates the metabolic activities of 1,432 genes via a network of 2,792 metabolites produced through 6,079 reactions distributed across six subcellular compartments. Growth was simulated under different steady-state light conditions (5-200 μmol photons m−2 s−1) and in a batch culture progressing from exponential growth to nitrate-limitation and nitrogen-starvation. We used the model to examine the dissipation of reductants generated through light-dependent processes and found that when available, nitrate assimilation is an important means of dissipating reductants in the plastid; under nitrate-limiting conditions, sulfate assimilation plays a similar role. The use of either nitrate or sulfate uptake to balance redox reactions leads to the secretion of distinct organic nitrogen and sulfur compounds. Such compounds can be accessed by bacteria in the surface ocean. The model of the diatom Thalassiosira pseudonana provides a mechanistic explanation for the production of ecologically and climatologically relevant compounds that may serve as the basis for intricate, cross-kingdom microbial networks. Diatom metabolism has an important influence on global biogeochemistry; metabolic models of marine microorganisms link genes to ecosystems and may be key to integrating molecular data with models of ocean biogeochemistry.

scholarly journals Biotransformation Mechanism of Inorganic Selenium into Selenomethionine and Selenocysteine by Saccharomyces Boulardii: In Silico Study

2021 ◽  
Author(s):  
Lourdes González-Salitre ◽  
Alma Delia Román-Gutiérrez ◽  
Gabriela Mariana Rodríguez-Serrano ◽  
Judith Jaimez-Ordaz ◽  
Mirandeli Bautista-Ávila ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
In Silico ◽  
Metabolic Model ◽  
Saccharomyces Boulardii ◽  
Orthologous Genes ◽  
Organic Species ◽  
Inorganic Selenium ◽  
In Silico Study ◽  
Probiotic Yeast ◽  
Genome Scale

Abstract The biosynthesis of inorganic selenium into seleno amino acids has been studied in recent years. Thus, it has been reported that Saccharomyces cerevisiae bioaccumulates selenium from the metabolism of inorganic selenium. Based on the studies conducted, several authors have proposed a biotransformation metabolism of selenate into selenomethionine or selenocysteine. However, the pathway in different yeast is unknown. Therefore, and given the relevance of Saccharomyces boulardii as probiotic yeast, this study aims to propose the pathway used by S. boulardii to biosynthesize inorganic selenium into organic species. A comparative in silico study was performed for Saccharomyces boulardii ASM141397V1 with the genome-scale metabolic model of Saccharomyces cerevisiae S288C. Orthologous genes were identified using BLASTp of NCBI. In addition, a circular representation was done using CIRCOS software. The metabolic pathway for the assimilation of selenium was proposed based on the results obtained

scholarly journals Genome-scale metabolic model of the diatom Thalassiosira pseudonana highlights the importance of nitrogen and sulfur metabolism in redox balance

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0241960
Author(s):  
Helena M. van Tol ◽  
E. Virginia Armbrust
Keyword(s):  
Organic Matter ◽  
Sulfur Metabolism ◽  
Reducing Power ◽  
Metabolic Model ◽  
Redox Balance ◽  
Thalassiosira Pseudonana ◽  
Cellular Damage ◽  
Marine Microorganisms ◽  
A Genome ◽  
Genome Scale

Diatoms are unicellular photosynthetic algae known to secrete organic matter that fuels secondary production in the ocean, though our knowledge of how their physiology impacts the composition of dissolved organic matter remains limited. Like all photosynthetic organisms, their use of light for energy and reducing power creates the challenge of avoiding cellular damage. To better understand the interplay between redox balance and organic matter secretion, we reconstructed a genome-scale metabolic model of Thalassiosira pseudonana strain CCMP 1335, a model for diatom molecular biology and physiology, with a 60-year history of studies. The model simulates the metabolic activities of 1,432 genes via a network of 2,792 metabolites produced through 6,079 reactions distributed across six subcellular compartments. Growth was simulated under different steady-state light conditions (5–200 μmol photons m-2 s-1) and in a batch culture progressing from exponential growth to nitrate-limitation and nitrogen-starvation. We used the model to examine the dissipation of reductants generated through light-dependent processes and found that when available, nitrate assimilation is an important means of dissipating reductants in the plastid; under nitrate-limiting conditions, sulfate assimilation plays a similar role. The use of either nitrate or sulfate uptake to balance redox reactions leads to the secretion of distinct organic nitrogen and sulfur compounds. Such compounds can be accessed by bacteria in the surface ocean. The model of the diatom Thalassiosira pseudonana provides a mechanistic explanation for the production of ecologically and climatologically relevant compounds that may serve as the basis for intricate, cross-kingdom microbial networks. Diatom metabolism has an important influence on global biogeochemistry; metabolic models of marine microorganisms link genes to ecosystems and may be key to integrating molecular data with models of ocean biogeochemistry.

scholarly journals Transcriptomic and Proteomic Approach for Understanding the Molecular Basis of Adaptation of Saccharomyces cerevisiae to Wine Fermentation

2006 ◽  
Vol 72 (1) ◽  
pp. 836-847 ◽  
Author(s):  
Aurora Zuzuarregui ◽  
Lucía Monteoliva ◽  
Concha Gil ◽  
Marcel·lí del Olmo
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stress Responses ◽  
Molecular Basis ◽  
Alcoholic Fermentation ◽  
Sulfur Metabolism ◽  
Secondary Compounds ◽  
Relative Increase ◽  
Yeast Cells ◽  
Nitrogen Catabolite Repression ◽  
Proteomic Approach

ABSTRACT Throughout alcoholic fermentation, Saccharomyces cerevisiae cells have to cope with several stress conditions that could affect their growth and viability. In addition, the metabolic activity of yeast cells during this process leads to the production of secondary compounds that contribute to the organoleptic properties of the resulting wine. Commercial strains have been selected during the last decades for inoculation into the must to carry out the alcoholic fermentation on the basis of physiological traits, but little is known about the molecular basis of the fermentative behavior of these strains. In this work, we present the first transcriptomic and proteomic comparison between two commercial strains with different fermentative behaviors. Our results indicate that some physiological differences between the fermentative behaviors of these two strains could be related to differences in the mRNA and protein profiles. In this sense, at the level of gene expression, we have found differences related to carbohydrate metabolism, nitrogen catabolite repression, and response to stimuli, among other factors. In addition, we have detected a relative increase in the abundance of proteins involved in stress responses (the heat shock protein Hsp26p, for instance) and in fermentation (in particular, the major cytosolic aldehyde dehydrogenase Ald6p) in the strain with better behavior during vinification. Moreover, in the case of the other strain, higher levels of enzymes required for sulfur metabolism (Cys4p, Hom6p, and Met22p) are observed, which could be related to the production of particular organoleptic compounds or to detoxification processes.

scholarly journals Functional cooperation of the glycine synthase-reductase and Wood–Ljungdahl pathways for autotrophic growth of Clostridium drakei

2020 ◽  
Vol 117 (13) ◽  
pp. 7516-7523 ◽  
Author(s):  
Yoseb Song ◽  
Jin Soo Lee ◽  
Jongoh Shin ◽  
Gyu Min Lee ◽  
Sangrak Jin ◽  
...  
Keyword(s):  
Reducing Power ◽  
Gene Clusters ◽  
Metabolic Model ◽  
Growth Conditions ◽  
Cellular Growth ◽  
Autotrophic Growth ◽  
Acetyl Coa ◽  
Biochemical Assays ◽  
Genes Encoding ◽  
Genome Scale

Among CO2-fixing metabolic pathways in nature, the linear Wood–Ljungdahl pathway (WLP) in phylogenetically diverse acetate-forming acetogens comprises the most energetically efficient pathway, requires the least number of reactions, and converts CO2 to formate and then into acetyl-CoA. Despite two genes encoding glycine synthase being well-conserved in WLP gene clusters, the functional role of glycine synthase under autotrophic growth conditions has remained uncertain. Here, using the reconstructed genome-scale metabolic model iSL771 based on the completed genome sequence, transcriptomics, 13C isotope-based metabolite-tracing experiments, biochemical assays, and heterologous expression of the pathway in another acetogen, we discovered that the WLP and the glycine synthase pathway are functionally interconnected to fix CO2, subsequently converting CO2 into acetyl-CoA, acetyl-phosphate, and serine. Moreover, the functional cooperation of the pathways enhances CO2 consumption and cellular growth rates via bypassing reducing power required reactions for cellular metabolism during autotrophic growth of acetogens.

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