Integrated Analysis Of Metabolic Phenotypes In Saccharomyces Cerevisiae

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Xylose-induced dynamic effects on metabolism and gene

control. Genome-scale dynamic flux balance analysis models were simulated to analyse the metabolic dynamics of S. cerevisiae. The simulations quantitatively estimated xylose-dependent flux dynamics and challenged the utilisation of the metabolic network. A relative increase in xylose utilisation was predicted to induce the bi-

A Minimal Set of Glycolytic Genes Reveals Strong Redundancies

of the yeast Saccharomyces cerevisiae, an intensively investigated model in eukaryotic evolutionary biology. A whole-genome du-plication event (WGD) in an ancestor of S.cerevisiae, ca. 100 mil-lionyearsago,wasfollowedbylossofca.90%oftheresultinggene duplications (4, 5). Despite the long time interval that separates

Dynamic Analysis of Integrated Signaling, Metabolic, and

Dynamic Analysis of Integrated Signaling, Metabolic, and simulates cellular phenotypes arising from integrated networks. of the single-cell eukaryotic organism Saccharomyces cerevisiae

An integrated approach to characterize genetic interaction

cerevisiae metabolic network, which consists of 1,412 reactions and accounts for 904 genes10. Genetic interaction data has been generated by large-scale synthetic genetic array (SGA) technology15. First, we performed new screens to construct a map that covers all major metabolic subsystems, except for transfer RNA aminoacylation.

Reverse engineering of industrially relevant phenotypes in yeast

metabolic engineering not only increases the understanding of the obtained phenotypes, but also makes it possible to combine traits in other hosts or protect the resulting intellectual property. The major challenge in reverse metabolic engineering is to identify the genetic changes that contribute to the desired phenotype.

Whole genome sequencing of Saccharomyces cerevisiae: from

isms, including S. cerevisiae strain S288c, the first eukar-yote genome sequence reported, provided a framework for gene annotation through functional genomics. More relevant to metabolic engineering, an annotated genome sequence was a prerequisite for genome-scale metabolic network reconstructions [9,10]. Such reconstructions


Fig.1 The concept of inverse metabolic engineering with multiple omics analyses. 2.1 Strains The laboratory strains S. cerevisiae FY834 and the brewing strain S. cerevisiae IFO2347 (Kyokai No. 7, used for sake brewing) were used for DNA microarray analysis and the construction of recombinant yeast strains. For analysis of the ethanol

Metabolic Engineering Strategies in Diatoms Reveal Unique

to well-established chassis, Escherichia coli and Saccharomyces cerevisiae. Such traits include its robustness and scalability for industrial-scale growth (Hamilton et al., 2015); and unlike bacteria and yeast species its ability to fix carbon via photosynthesis for cheaper culture conditions. There is also

Ontology-based cross-species integration and analysis of

Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes Georgios V. Gkoutos and Robert Hoehndorf Department of Genetics, University of Cambridge, Downing Street, Cambridge, Cambridge CB2 3EH, UK ABSTRACT Ontologies are widely used in the biomedical community for annotation and integration of databases.

Dissertation VTT PUBLICATIONS 724

analysis utilises directly the 13C-labelling data and metabolic network models to solve ratios of converging fluxes. In this thesis the local flux ratio analysis has been extended and applied to analysis of phenotypes of biotechnologically important yeasts Saccharomyces cerevisiae and Pichia pastoris, and a fungus Trichoderma reesei. Oxygen de-

Genome-scale Bacterial Transcriptional Regulatory Networks

data, we discuss how regulatory networks can be reconstructed and integrated with metabolic models to improve model predictions and performance. We also explore the impact these integrated models can have in simulating phenotypes, optimizing the production of compounds of interest, or paving the way to a whole-cell model. Keywords

Integration of transcription and flux data reveals molecular

oxygen-dependent phenotypes of Saccharomyces cerevisiae The detection of molecular paths was performed in an integrated genome-scale metabolic and analysis [3]. Full interconnectivity of

Metabolic and Developmental Effects Resulting from Deletion

In Saccharomyces cerevisiae the mitochondrial Cit1 is the major citrate synthase of the TCA cycle. An additional en-zyme, Cit2, is peroxisomally localized via a C-terminal perox-isomal targeting sequence (PTS1) (29). In response to mito-chondrial dysfunction CIT2 is upregulated via the retrograde response mediated by RTG1,-2, and-3, while

Metabolic network modeling with model organisms

Saccharomyces cerevisiae coli n/a B,D,I B,D,I B,I,A B,I B,D B,D % Orthologs in human model Current Opinion in Chemical Biology Model organisms reviewed. Percentage of genes in a human genome scale metabolic network model [4 ] that have orthologs to each model organism is shown based on Ref. [31]. This number is not available for E. coli.

Metabolic Constraint-Based Refinement of Transcriptional

GEMINI to create an integrated metabolic-regulatory network model for Saccharomyces cerevisiae involving 25,000 regulatory interactions controlling 1597 metabolic reactions. The model quantitatively predicts TF knockout phenotypes in new conditions (p-value=10214) and revealed potential condition-specific regulatory mechanisms. Our results

Environmental systems biology of cold-tolerant phenotype in

tolerant) and S. cerevisiae 96.2 (thermo-tolerant). Using two different systems approaches, i. thermodynamic-based analysis of a genome-scale metabolic model of S. cerevisiae and ii. large-scale competition experiment of the yeast heterozygote mutant collection, genes and pathways important for the growth at low temperature were identi-fied.

Development of Bottom-Fermenting Saccharomyces Strains That

analyzed for similar metabolic fluxes. One promising mutant produced much higher levels of SO 2 than the parent but produced parental levels of H 2 S. The bottom-fermenting yeast Saccharomyces pastorianus is used to produce beer and has been proposed to be a natural hybrid between Saccharomyces cerevisiae and Saccharomyces bayanus (30). Bottom

Large-scale functional analysis of the roles of

regulate various metabolic enzymes, we performed an enrichment analysis of the KEGG pathway annotations for metabolites that were altered in ki-nase and phosphatase deletion strains. For about 80% of the kinase and phosphatase deletion strains with detectable metabolic changes, we found at least one significantly enriched pathway (table S7).

Chalmers Publication Library

The genome-scale metabolic model ilN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism This document has been downloaded from Chalmers Publication Library (CPL). It is the author´s version of a work that was accepted for publication in: BMC Systems Biology Citation for the published paper:

BMC Genomics BioMed Central - COnnecting REpositories

Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae Natalie C Duarte 1, Bernhard Ø Palsson and Pengcheng Fu*2 Address: 1Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA and 2Department

Systems-Level Engineering of Nonfermentative Metabolism in Yeast

endogenous one-carbon (C1) metabolism in yeast. We used constraint-based metabolic modeling and computer-aided gene knockout simulations to identify five genes (ALT2, FDH1, FDH2, FUM1, and ZWF1), which, when deleted in combination, predicted formic acid secretion in Saccharomyces cerevisiae under aerobic growth conditions.

Metabolic Changes Induced by Deletion of Transcriptional

Sep 29, 2020 Metabolic Changes Induced by Deletion of Transcriptional Regulator GCR2 in Xylose-Fermenting Saccharomyces cerevisiae Minhye Shin 1 and Soo Rin Kim 2,* 1 Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea; [email protected]

WIT: integrated system for high-throughput genome sequence

An important stage of genome analysis is the integration of gene assignments into an organism-specific overview via so-called functional reconstruction (15), which is the conceptual assembly of metabolic pathways, transport units and signal transduction pathways. It allows reconciliation of inconsistencies between different types of analysis, and

PROCEEDINGS Open Access Ontology-based cross-species

species integration of yeast phenotypes and a similarity-based comparison of yeast phenotypes across species available in the PhenomeBrowser [22]. Materials and methods Saccharomyces Genome Database The Saccharomyces Genome Database (SGD) is a freely available collection of genetic and molecular information aboutSaccharomyces cerevisiae

Integrated analysis of regulatory and metabolic networks

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae Markus J. Herrgård, Baek-Seok Lee,1 Vasiliy Portnoy, and Bernhard Ø. Palsson2 Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412, USA

Advancing Metabolic Engineering through Combination of

through integrated systems level analysis Kuk-Ki Hong, Wanwipa Vongsangnak, Goutham N. Vemuri and Jens Nielsen Proc. Natl. Acad. Sci. USA. 2011 Jul 19; 108(29):12179 84. II. Recovery of phenotypes obtained by adaptive evolution through inverse metabolic engineering Kuk-Ki Hong and Jens Nielsen Accepted in Appl. Environ. Microbiol. 2012 III.

Model-driven analysis of experimentally determined growth

Results: In this study, we measured growth phenotypes of 465 Saccharomyces cerevisiae gene deletion mutants under 16 metabolically relevant conditions and integrated them with the corresponding flux balance model predictions. We first used discordance between experimental

Dissertation VTT PUBLICATIONS 724 - TKK

analysis utilises directly the 13C-labelling data and metabolic network models to solve ratios of converging fluxes. In this thesis the local flux ratio analysis has been extended and applied to analysis of phenotypes of biotechnologically important yeasts Saccharomyces cerevisiae and Pichia pastoris, and a fungus Trichoderma reesei. Oxygen de-

Unravelling evolutionary strategies of yeast for improving

performed a systems-level inquiry into the metabolic changes oc-curring in the yeast Saccharomyces cerevisiae as a result of its ad-aptive evolution to increase its specific growth rate on galactose and related these changes to the acquired phenotypic properties. Three evolved mutants (62A, 62B, and 62C) with higher specific

Protein Abundance Prediction Through Machine Learning Methods

Sep 17, 2020 (GECKO models) have only been reconstructed for Saccharomyces cerevisiae (10, 11) and Bacillus subtilis (12). The integration of omics data to GEMs, especially protein abundance, can be useful to improve simulations. For example, the S. cerevisiae iMM904 model, which is integrated with proteomic

Saccharomyces cerevisiaephenotypes can be predicted by using

phenotypes were consistent with experimental observations. Thus, constraint-based analysis of a genome-scale metabolic net-work for the eukaryotic S. cerevisiae allows for computation of its integrated functions, producing in silico results that were consis-tent with observed phenotypic functions for 70 80% of the conditions considered.

Profiling of Cytosolic and Peroxisomal Acetyl-CoA Metabolism

Metabolism in Saccharomyces cerevisiae Yun Chen, Verena Siewers, Jens Nielsen* Department of Chemical and Biological Engineering, Chalmers University of Technology, Go¨teborg, Sweden Abstract As a key intracellular metabolite, acetyl-coenzyme A (acetyl-CoA) plays a major role in various metabolic pathways that link anabolism and catabolism.

RESEARCH Open Access Systematic and evolutionary engineering

lignocellulose by the yeast Saccharomyces cerevisiae [1,2]. Several metabolic deficiencies in this yeast, including the lack of an endogenous pathway for xylose catabolism, require metabolic engineering. Many efforts have been reported that introduce heterologous xylose catabolism, such as the oxidoreductase pathway from Scheffersomyces

The genome-scale metabolic model iIN800 of Saccharomyces

The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism Intawat Nookaew 1, Michael C Jewett5,6, Asawin Meechai , Chinae Thammarongtham2, Kobkul Laoteng2, Supapon Cheevadhanarak3, Jens Nielsen*5,7 and Sakarindr Bhumiratana*1,2,4

Development of Saccharomyces cerevisiae as a Model Pathogen

Saccharomyces cerevisiae, a close relative of the pathogenic Candida species, is an emerging opportunistic pathogen. An isogenic series of S. cerevisiae strains, derived from a human clinical isolate, were used to examine the role of evolutionarily conserved pathways in fungal survival in a mouse host. As is the

RESEARCH ARTICLE Open Access Bridging the gap between gene

phenotypic alterations of Saccharomyces cerevisiae treated with weak organic acids (i.e., acetate, benzoate, propionate, or sorbate) and the histidine synthesis inhibitor 3-aminotriazole under steady-state conditions. We found that the transcriptional response led to alterations in yeast metabolism that mimicked measured metabolic fluxes and

Integrated analysis of isopentenyl pyrophosphate (IPP

product toxicity in common industrial hosts such as Escherichia coli and Saccharomyces cerevisiae (Mukhopadhyay, 2015). Assessment of product or intermediate toxicity is challenging, particularly in an engineered host that produces the molecules in vivo. In engineered microbes harboring

Metabolic Engineering of Wine Strains of Saccharomyces cerevisiae

Aug 20, 2020 Metabolic Engineering of Wine Strains of Saccharomyces cerevisiae Mikhail A. Eldarov and Andrey V. Mardanov * Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] * Correspondence: [email protected]

Quantitative Trait Loci (QTL)-Guided Metabolic Engineering of

Here, we devised an integrated approach for QTL-guided metabolic engineering, and we used our method to engineer hydrolysate tolerance in S. cerevisiae. Our methodology integrates high-resolution QTL mapping (Figure 1A), bulk Reciprocal Hemizygosity Analysis (bRHA) (Figure 1B), and a Cas9-mediated method for efficient allele replacements

Identification of new Saccharomyces cerevisiae variants of

Identification of new Saccharomyces cerevisiae variants of the MET2 and SKP2 genes controlling the sulfur assimilation pathway and the production of undesirable sulfur compounds during alcoholic fermentation Jessica Noble, Isabelle Sanchez, Bruno Blondin To cite this version: Jessica Noble, Isabelle Sanchez, Bruno Blondin.