A network perspective on the evolution of metabolism by gene duplication

Díaz-Mejía, J. Javier; Pérez‐Rueda, Ernesto; Segovia, Lorenzo

doi:10.1186/gb-2007-8-2-r26

Cited by 54 publications

(57 citation statements)

References 36 publications

(42 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…[4,5], for example). In particular, several studies, until now, have discussed possible mechanisms underlying the evolution of metabolic networks [6][7][8] and their contribution to environmental adaptation (reviewed in Refs. [9,10]).…”

Section: Introductionmentioning

confidence: 99%

Metabolic network modularity arising from simple growth processes

Takemoto

2012

Phys. Rev. E

View full text Add to dashboard Cite

Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous studies have suggested a theoretical model, which proposes that a change in the evolutionary goal (system-specific purpose) increases network modularity, and this hypothesis was supported by statistical data analysis. Nevertheless, further investigation has uncovered additional possibilities that might explain the origin of network modularity. In this work we propose an evolving network model without tuning parameters to describe metabolic networks. We demonstrate, quantitatively, that metabolic network modularity can arise from simple growth processes, independent of the change in the evolutionary goal. Our model is applicable to a wide range of organisms and appears to suggest that metabolic network modularity can be more simply determined than previously thought. Nonetheless, our proposition does not serve to contradict the previous model; it strives to provide an insight from a different angle in the ongoing efforts to understand metabolic evolution, with the hope of eventually achieving the synthetic engineering of metabolic networks.

show abstract

Section: Introductionmentioning

confidence: 99%

Metabolic network modularity arising from simple growth processes

Takemoto

2012

Phys. Rev. E

View full text Add to dashboard Cite

show abstract

“…) and the fitness effect of its duplication. That such relations exist is already suggested by an analysis of duplicates in metabolic networks (Diaz-Mejia et al, 2007).…”

Section: Reconsidering Fitness Effects Of Duplications In the Contextmentioning

confidence: 96%

Fate of a Duplicate in a Network Context

Soyer

2010

Evolution After Gene Duplication

View full text Add to dashboard Cite

“…Since such similar enzymes often result from gene duplication, more duplicated genes may increase the enzymatic network modularity (Q ud ). In fact, Díaz-Mejía et al (Díaz-Mejía et al, 2007) reported a high retention of duplicates within functional modules in enzymatic networks. This fact also explains the observed positive relationship between enzymatic network modularity and the fraction of duplicated genes in flies (Figure 3).…”

Section: Discussionmentioning

confidence: 99%

“…In addition to the potential effect on habitat variability in promoting network modularity, an association between gene duplication and habitat variability has also been observed. Given that gene duplication also influences the metabolic network structure (Barabási & Oltvai, 2004;Díaz-Mejía, Pérez-Rueda, & Segovia, 2007;Papp, Pál, & Hurst, 2004;Takemoto, 2012a), it is reasonable to hypothesize that habitat variability may be linked to not only gene duplication but also metabolic network modularity. To investigate these relationships, data related to habitat variability were collected from the published literature; data were collected only from species for which metabolic network data are also available (see Section 2).…”

Section: Introductionmentioning

confidence: 99%

Habitat variability does not generally promote metabolic network modularity in flies and mammals

Takemoto

2016

Biosystems

View full text Add to dashboard Cite

The evolution of species habitat range is an important topic over a wide range of research fields. In higher organisms, habitat range evolution is generally associated with genetic events such as gene duplication. However, the specific factors that determine habitat variability remain unclear at higher levels of biological organization (e.g., biochemical networks). One widely accepted hypothesis developed from both theoretical and empirical analyses is that habitat variability promotes network modularity; however, this relationship has not yet been directly tested in higher organisms. Therefore, I investigated the relationship between habitat variability and metabolic network modularity using compound and enzymatic networks in flies and mammals. Contrary to expectation, there was no clear positive correlation between habitat variability and network modularity. As an exception, the network modularity increased with habitat variability in the enzymatic networks of flies. However, the observed association was likely an artifact, and the frequency of gene duplication appears to be the main factor contributing to network modularity. These findings raise the question of whether or not there is a general mechanism for habitat range expansion at a higher level (i.e., above the gene scale). This study suggests that the currently widely accepted hypothesis for habitat variability should be reconsidered.

show abstract

A network perspective on the evolution of metabolism by gene duplication

Cited by 54 publications

References 36 publications

Metabolic network modularity arising from simple growth processes

Metabolic network modularity arising from simple growth processes

Fate of a Duplicate in a Network Context

Habitat variability does not generally promote metabolic network modularity in flies and mammals

Contact Info

Product

Resources

About