PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
PLoS One. 2011;6(10):e25874. doi: 10.1371/journal.pone.0025874. Epub 2011 Oct 6.
Network modularity is an important structural feature in metabolic networks. A previous study suggested that the variability in natural habitat promotes metabolic network modularity in bacteria. However, since many factors influence the structure of the metabolic network, this phenomenon might be limited and there may be other explanations for the change in metabolic network modularity. Therefore, we focus on archaea because they belong to another domain of prokaryotes and show variability in growth conditions (e.g., trophic requirement and optimal growth temperature), but not in habitats because of their specialized growth conditions (e.g., high growth temperature). The relationship between biological features and metabolic network modularity is examined in detail. We first show the absence of a relationship between network modularity and habitat variability in archaea, as archaeal habitats are more limited than bacterial habitats. Although this finding implies the need for further studies regarding the differences in network modularity, it does not contradict previous work. Further investigations reveal alternative explanations. Specifically, growth conditions, trophic requirement, and optimal growth temperature, in particular, affect metabolic network modularity. We have discussed the mechanisms for the growth condition-dependant changes in network modularity. Our findings suggest different explanations for the changes in network modularity and provide new insights into adaptation and evolution in metabolic networks, despite several limitations of data analysis.
网络模块性是代谢网络的一个重要结构特征。之前的研究表明，自然栖息地的变化促进了细菌代谢网络的模块性。然而，由于许多因素影响代谢网络的结构，这种现象可能是有限的，代谢网络模块性的变化可能有其他解释。因此，我们专注于古菌，因为它们属于原核生物的另一个领域，并且在生长条件（例如营养需求和最佳生长温度）方面表现出可变性，但由于其特殊的生长条件（例如高温），在栖息地方面没有可变性。详细研究了生物特征与代谢网络模块性之间的关系。我们首先表明，在古菌中，网络模块性与栖息地可变性之间不存在关系，因为古菌的栖息地比细菌的栖息地更有限。尽管这一发现意味着需要进一步研究网络模块性的差异，但它并没有与之前的工作相矛盾。进一步的调查揭示了替代解释。具体来说，生长条件、营养需求和最佳生长温度，特别是，影响代谢网络模块性。我们讨论了生长条件依赖性网络模块性变化的机制。尽管数据分析存在一些限制，但我们的研究结果为代谢网络的适应和进化提供了不同的解释，并为代谢网络的适应和进化提供了新的见解。
