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. 2007 Sep 23:7:169.
doi: 10.1186/1471-2148-7-169.

Environmental variability and modularity of bacterial metabolic networks

Merav Parter  1 , Nadav Kashtan, Uri Alon
Affiliations

Environmental variability and modularity of bacterial metabolic networks

Merav Parter et al. BMC Evol Biol. .

Abstract

Background: Biological systems are often modular: they can be decomposed into nearly-independent structural units that perform specific functions. The evolutionary origin of modularity is a subject of much current interest. Recent theory suggests that modularity can be enhanced when the environment changes over time. However, this theory has not yet been tested using biological data.

Results: To address this, we studied the relation between environmental variability and modularity in a natural and well-studied system, the metabolic networks of bacteria. We classified 117 bacterial species according to the degree of variability in their natural habitat. We find that metabolic networks of organisms in variable environments are significantly more modular than networks of organisms that evolved under more constant conditions.

Conclusion: This study supports the view that variability in the natural habitat of an organism promotes modularity in its metabolic network and perhaps in other biological systems.

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Figures

Figure 1
Figure 1
Relation between environmental variability and a. Mean fractional number of transcription factors out of the total number of genes in the genome. b. Mean metabolic network size (giant component). Error bars represent standard errors. Abbreviation: O-Obligate, S-Specialized, AQ-Aquatic, F-Facultative, M-Multiple, T-Terrestrial. Groups ordered along x-axis according to their predicted level of variability.
Figure 2
Figure 2
Relation between environmental variability and modularity. Normalized modularity measure (Qm) of bacterial metabolic networks versus the environmental class of the organism. Environments are ordered according to their variability ranging from O (obligate), the least variable to T (terrestrial), the most variable. Mean and standard error of Qm are presented for each environmental class.
Figure 3
Figure 3
Visualization of metabolic networks for a) E. coli and b) Buchnera aphidicola. The two networks consist of the same number of nodes (n = 89 metabolites), achieved by reducing E. coli network (see additional file 2, section 5).
Figure 4
Figure 4
Cartographic representation for the metabolic networks of a. E. coli and b. Buchnera aphidicola. Each circle corresponds to a structural module. Colors represent KEGG pathway classification, where the fraction of each class is proportional to the significance level of that category in the module nodes obtained from a hypergeometric test. Circle size is proportional to module's size and the thickness of edges proportional to the number of interactions between two modules. In E. coli most of the modules are functionally pure, and each metabolic class can be assigned to a specific structural module. In Buchnera network, modules are less pure and show more mixture of different functions. In three models, however, pureness of amino acid metabolism can be detected (e.g. the basis for the symbiosis with aphids)
Figure 5
Figure 5
Illustration of a mechanism that reduces modularity. The connection between purine and histidine pathways is presented for a. E. coli and b. Buchnera sp. APS. Whereas in E. coli the pathways are separated, in Buchnera the pathways are partially combined [51].
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References

    1. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature. 1999;402:C47–52. doi: 10.1038/35011540. - DOI - PubMed
    1. Wagner G, Schlosser G. Modularity in Development and Evolution. University of Chicago Press; 2004.
    1. Alon U. An Introduction to Systems Biology: Design Principles of Biological circuits. 1. Chapman & Hall/CRC; 2006.
    1. Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED. Metabolic network structure determines key aspects of functionality and regulation. Nature. 2002;4:190–193. doi: 10.1038/nature01166. - DOI - PubMed
    1. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL. Hierarchical organization of modularity in metabolic networks. Science. 2002;297:1551–1555. doi: 10.1126/science.1073374. - DOI - PubMed

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