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Evolutionary constraints permeate large metabolic networks


Wagner, A (2009). Evolutionary constraints permeate large metabolic networks. BMC Evolutionary Biology, 9:231.

Abstract

BACKGROUND: Metabolic networks show great evolutionary plasticity, because they can differ substantially even among closely related prokaryotes. Any one metabolic network can also effectively compensate for the blockage of individual reactions by rerouting metabolic flux through other pathways. These observations, together with the continual discovery of new microbial metabolic pathways and enzymes, raise the possibility that metabolic networks are only weakly constrained in changing their complement of enzymatic reactions. RESULTS: To ask whether this is the case, I characterized pairwise and higher-order associations in the co-occurrence of genes encoding metabolic enzymes in more than 200 completely sequenced representatives of prokaryotic genera. The majority of reactions show constrained evolution. Specifically, genes encoding most reactions tend to co-occur with genes encoding other reaction(s). Constrained reaction pairs occur in small sets whose number is substantially greater than expected by chance alone. Most such sets are associated with single biochemical pathways. The respective genes are not always tightly linked, which renders horizontal co-transfer of constrained reaction sets an unlikely sole cause for these patterns of association. CONCLUSION: Even a limited number of available genomes suffices to show that metabolic network evolution is highly constrained by reaction combinations that are favored by natural selection. With increasing numbers of completely sequenced genomes, an evolutionary constraint-based approach may enable a detailed characterization of co-evolving metabolic modules.

Abstract

BACKGROUND: Metabolic networks show great evolutionary plasticity, because they can differ substantially even among closely related prokaryotes. Any one metabolic network can also effectively compensate for the blockage of individual reactions by rerouting metabolic flux through other pathways. These observations, together with the continual discovery of new microbial metabolic pathways and enzymes, raise the possibility that metabolic networks are only weakly constrained in changing their complement of enzymatic reactions. RESULTS: To ask whether this is the case, I characterized pairwise and higher-order associations in the co-occurrence of genes encoding metabolic enzymes in more than 200 completely sequenced representatives of prokaryotic genera. The majority of reactions show constrained evolution. Specifically, genes encoding most reactions tend to co-occur with genes encoding other reaction(s). Constrained reaction pairs occur in small sets whose number is substantially greater than expected by chance alone. Most such sets are associated with single biochemical pathways. The respective genes are not always tightly linked, which renders horizontal co-transfer of constrained reaction sets an unlikely sole cause for these patterns of association. CONCLUSION: Even a limited number of available genomes suffices to show that metabolic network evolution is highly constrained by reaction combinations that are favored by natural selection. With increasing numbers of completely sequenced genomes, an evolutionary constraint-based approach may enable a detailed characterization of co-evolving metabolic modules.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Department of Biochemistry
07 Faculty of Science > Department of Biochemistry
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:2009
Deposited On:02 Dec 2009 09:17
Last Modified:03 Aug 2017 15:09
Publisher:BioMed Central
ISSN:1471-2148
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.1186/1471-2148-9-231
PubMed ID:19747381

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