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Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks

Oxygen is thought to promote species and biomolecule diversity. Previous studies have suggested that oxygen expands metabolic networks by acquiring metabolites with different chemical properties (higher hydrophobicity, for example). However, such conclusions are typically based on biased evaluation,...

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Detalles Bibliográficos
Autores principales: Takemoto, Kazuhiro, Yoshitake, Ikumi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937826/
https://www.ncbi.nlm.nih.gov/pubmed/24958261
http://dx.doi.org/10.3390/metabo3040979
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author Takemoto, Kazuhiro
Yoshitake, Ikumi
author_facet Takemoto, Kazuhiro
Yoshitake, Ikumi
author_sort Takemoto, Kazuhiro
collection PubMed
description Oxygen is thought to promote species and biomolecule diversity. Previous studies have suggested that oxygen expands metabolic networks by acquiring metabolites with different chemical properties (higher hydrophobicity, for example). However, such conclusions are typically based on biased evaluation, and are therefore non-conclusive. Thus, we re-investigated the effect of oxygen on metabolic evolution using a phylogenetic comparative method and metadata analysis to reduce the bias as much as possible. Notably, we found no difference in metabolic network expansion between aerobes and anaerobes when evaluating phylogenetic relationships. Furthermore, we showed that previous studies have overestimated or underestimated the degrees of differences in the chemical properties (e.g., hydrophobicity) between oxic and anoxic metabolites in metabolic networks of unicellular organisms; however, such overestimation was not observed when considering the metabolic networks of multicellular organisms. These findings indicate that the contribution of oxygen to increased chemical diversity in metabolic networks is lower than previously thought; rather, phylogenetic signals and cell-cell communication result in increased chemical diversity. However, this conclusion does not contradict the effect of oxygen on metabolic evolution; instead, it provides a deeper understanding of how oxygen contributes to metabolic evolution despite several limitations in data analysis methods.
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spelling pubmed-39378262014-05-27 Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks Takemoto, Kazuhiro Yoshitake, Ikumi Metabolites Article Oxygen is thought to promote species and biomolecule diversity. Previous studies have suggested that oxygen expands metabolic networks by acquiring metabolites with different chemical properties (higher hydrophobicity, for example). However, such conclusions are typically based on biased evaluation, and are therefore non-conclusive. Thus, we re-investigated the effect of oxygen on metabolic evolution using a phylogenetic comparative method and metadata analysis to reduce the bias as much as possible. Notably, we found no difference in metabolic network expansion between aerobes and anaerobes when evaluating phylogenetic relationships. Furthermore, we showed that previous studies have overestimated or underestimated the degrees of differences in the chemical properties (e.g., hydrophobicity) between oxic and anoxic metabolites in metabolic networks of unicellular organisms; however, such overestimation was not observed when considering the metabolic networks of multicellular organisms. These findings indicate that the contribution of oxygen to increased chemical diversity in metabolic networks is lower than previously thought; rather, phylogenetic signals and cell-cell communication result in increased chemical diversity. However, this conclusion does not contradict the effect of oxygen on metabolic evolution; instead, it provides a deeper understanding of how oxygen contributes to metabolic evolution despite several limitations in data analysis methods. MDPI 2013-10-16 /pmc/articles/PMC3937826/ /pubmed/24958261 http://dx.doi.org/10.3390/metabo3040979 Text en © 2013 by the authors; licensee MDPI, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0/ This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Takemoto, Kazuhiro
Yoshitake, Ikumi
Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks
title Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks
title_full Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks
title_fullStr Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks
title_full_unstemmed Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks
title_short Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks
title_sort limited influence of oxygen on the evolution of chemical diversity in metabolic networks
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937826/
https://www.ncbi.nlm.nih.gov/pubmed/24958261
http://dx.doi.org/10.3390/metabo3040979
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