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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,...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2013
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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. |
format | Online Article Text |
id | pubmed-3937826 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT takemotokazuhiro limitedinfluenceofoxygenontheevolutionofchemicaldiversityinmetabolicnetworks AT yoshitakeikumi limitedinfluenceofoxygenontheevolutionofchemicaldiversityinmetabolicnetworks |