Structural analyses of a hypothetical minimal metabolism

被引:31
作者
Gabaldon, Toni
Pereto, Juli
Montero, Francisco
Gil, Rosario
Latorre, Amparo
Moya, Andres
机构
[1] Univ Valencia, Inst Cavanilles Biodivers & Biol Evolut, Valencia 46071, Spain
[2] Ctr Invest Principe Felipe, Bioinformat Dept, Valencia 46013, Spain
[3] Univ Valencia, Dept Bioquim & Biol Mol, E-46100 Valencia, Spain
[4] Univ Valencia, Dept Genet, E-46100 Valencia, Spain
[5] Univ Complutense, Fac Quim, Dept Bioquim & Biol Mol 1, E-28040 Madrid, Spain
关键词
minimal genome; metabolic inference; elementary flux mode; scale-free network; network topology; power law;
D O I
10.1098/rstb.2007.2067
中图分类号
Q [生物科学];
学科分类号
07 [理学]; 0710 [生物学]; 09 [农学];
摘要
By integrating data from comparative genomics and large-scale deletion studies, we previously proposed a minimal gene set comprising 206 protein-coding genes. To evaluate the consistency of the metabolism encoded by such a minimal genome, we have carried out a series of computational analyses. Firstly, the topology of the minimal metabolism was compared with that of the reconstructed networks from natural bacterial genomes. Secondly, the robustness of the metabolic network was evaluated by simulated mutagenesis and, finally, the stoichiometric consistency was assessed by automatically deriving the steady-state solutions from the reaction set. The results indicated that the proposed minimal metabolism presents stoichiometric consistency and that it is organized as a complex power-law network with topological parameters falling within the expected range for a natural metabolism of its size. The robustness analyses revealed that most random mutations do not alter the topology of the network significantly, but do cause significant damage by preventing the synthesis of several compounds or compromising the stoichiometric consistency of the metabolism. The implications that these results have on the origins of metabolic complexity and the theoretical design of an artificial minimal cell are discussed.
引用
收藏
页码:1751 / 1762
页数:12
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