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Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations
Environmental perturbations are encountered by microorganisms regularly and will require metabolic adaptations to ensure an organism can survive in the newly presenting conditions. In order to study the mechanisms of metabolic adaptation in such conditions, various experimental and computational app...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10694557/ https://www.ncbi.nlm.nih.gov/pubmed/38048080 http://dx.doi.org/10.1093/bib/bbad439 |
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author | Carter, Elena Lucy Constantinidou, Chrystala Alam, Mohammad Tauqeer |
author_facet | Carter, Elena Lucy Constantinidou, Chrystala Alam, Mohammad Tauqeer |
author_sort | Carter, Elena Lucy |
collection | PubMed |
description | Environmental perturbations are encountered by microorganisms regularly and will require metabolic adaptations to ensure an organism can survive in the newly presenting conditions. In order to study the mechanisms of metabolic adaptation in such conditions, various experimental and computational approaches have been used. Genome-scale metabolic models (GEMs) are one of the most powerful approaches to study metabolism, providing a platform to study the systems level adaptations of an organism to different environments which could otherwise be infeasible experimentally. In this review, we are describing the application of GEMs in understanding how microbes reprogram their metabolic system as a result of environmental variation. In particular, we provide the details of metabolic model reconstruction approaches, various algorithms and tools for model simulation, consequences of genetic perturbations, integration of ‘-omics’ datasets for creating context-specific models and their application in studying metabolic adaptation due to the change in environmental conditions. |
format | Online Article Text |
id | pubmed-10694557 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-106945572023-12-05 Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations Carter, Elena Lucy Constantinidou, Chrystala Alam, Mohammad Tauqeer Brief Bioinform Review Environmental perturbations are encountered by microorganisms regularly and will require metabolic adaptations to ensure an organism can survive in the newly presenting conditions. In order to study the mechanisms of metabolic adaptation in such conditions, various experimental and computational approaches have been used. Genome-scale metabolic models (GEMs) are one of the most powerful approaches to study metabolism, providing a platform to study the systems level adaptations of an organism to different environments which could otherwise be infeasible experimentally. In this review, we are describing the application of GEMs in understanding how microbes reprogram their metabolic system as a result of environmental variation. In particular, we provide the details of metabolic model reconstruction approaches, various algorithms and tools for model simulation, consequences of genetic perturbations, integration of ‘-omics’ datasets for creating context-specific models and their application in studying metabolic adaptation due to the change in environmental conditions. Oxford University Press 2023-12-02 /pmc/articles/PMC10694557/ /pubmed/38048080 http://dx.doi.org/10.1093/bib/bbad439 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Review Carter, Elena Lucy Constantinidou, Chrystala Alam, Mohammad Tauqeer Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations |
title | Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations |
title_full | Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations |
title_fullStr | Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations |
title_full_unstemmed | Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations |
title_short | Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations |
title_sort | applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10694557/ https://www.ncbi.nlm.nih.gov/pubmed/38048080 http://dx.doi.org/10.1093/bib/bbad439 |
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