Sökning: WFRF:(Anton Petre Mihail 1989) >
Reconstruction of a...
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
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- Domenzain Del Castillo Cerecer, Iván, 1991 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology,Novo Nordisk Fonden,Novo Nordisk Foundation
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- Sánchez, Benjamín José, 1988 (författare)
- Danmarks Tekniske Universitet,Technical University of Denmark
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- Anton, Petre Mihail, 1989 (författare)
- Science for Life Laboratory (SciLifeLab),Chalmers tekniska högskola,Chalmers University of Technology
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- Kerkhoven, Eduard, 1985 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology,Novo Nordisk Fonden,Novo Nordisk Foundation
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- Millan-Oropeza, Aaron (författare)
- Université Paris-Saclay,University Paris-Saclay
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- Henry, Céline (författare)
- Université Paris-Saclay,University Paris-Saclay
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- Siewers, Verena, 1976 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology,Novo Nordisk Fonden,Novo Nordisk Foundation
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Morrissey, John P. (författare)
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- Sonnenschein, N. (författare)
- Danmarks Tekniske Universitet,Technical University of Denmark
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- Nielsen, Jens B, 1962 (författare)
- Novo Nordisk Fonden,Novo Nordisk Foundation,Chalmers tekniska högskola,Chalmers University of Technology,BioInnovation Institute (BII)
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(creator_code:org_t)
- 2022-06-30
- 2022
- Engelska.
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 13:1
- Relaterad länk:
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https://research.cha... (primary) (free)
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https://doi.org/10.1...
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https://research.cha...
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Abstract
Ämnesord
Stäng
- Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into such models was first enabled by the GECKO toolbox, allowing the study of phenotypes constrained by protein limitations. Here, we upgrade the toolbox in order to enhance models with enzyme and proteomics constraints for any organism with a compatible GEM reconstruction. With this, enzyme-constrained models for the budding yeasts Saccharomyces cerevisiae, Yarrowia lipolytica and Kluyveromyces marxianus are generated to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions reveal that upregulation and high saturation of enzymes in amino acid metabolism are common across organisms and conditions, suggesting the relevance of metabolic robustness in contrast to optimal protein utilization as a cellular objective for microbial growth under stress and nutrient-limited conditions. The functionality of GECKO is expanded with an automated framework for continuous and version-controlled update of enzyme-constrained GEMs, also producing such models for Escherichia coli and Homo sapiens. In this work, we facilitate the utilization of enzyme-constrained GEMs in basic science, metabolic engineering and synthetic biology purposes.
Ämnesord
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
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Domenzain Del Ca ...
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Sánchez, Benjamí ...
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Anton, Petre Mih ...
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Kerkhoven, Eduar ...
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Millan-Oropeza, ...
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Henry, Céline
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Siewers, Verena, ...
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Morrissey, John ...
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Sonnenschein, N.
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Nielsen, Jens B, ...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Biokemi och mole ...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Data och informa ...
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och Bioinformatik
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Chalmers tekniska högskola