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Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks
Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kawazu 680-4, Iizuka, Fukuoka 820-8502, Japan
* Author to whom correspondence should be addressed.
Received: 31 July 2013; in revised form: 9 October 2013 / Accepted: 11 October 2013 / Published: 16 October 2013
Abstract: 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.
Keywords: metabolism; chemoinformatics; environmental interaction; evolution
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MDPI and ACS Style
Takemoto, K.; Yoshitake, I. Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks. Metabolites 2013, 3, 979-992.
Takemoto K, Yoshitake I. Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks. Metabolites. 2013; 3(4):979-992.
Takemoto, Kazuhiro; Yoshitake, Ikumi. 2013. "Limited Influence of Oxygen on the Evolution of Chemical Diversity in Metabolic Networks." Metabolites 3, no. 4: 979-992.