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BMC Bioinformatics

, 5:15

First Online: 18 February 2004Received: 18 July 2003Accepted: 18 February 2004

Abstract

BackgroundThe two most common models for the evolution of metabolism are the patchwork evolution model, where enzymes are thought to diverge from broad to narrow substrate specificity, and the retrograde evolution model, according to which enzymes evolve in response to substrate depletion.
Analysis of the distribution of homologous enzyme pairs in the metabolic network can shed light on the respective importance of the two models.
We here investigate the evolution of the metabolism in E.
coli viewed as a single network using EcoCyc.

ResultsSequence comparison between all enzyme pairs was performed and the minimal path length MPL between all enzyme pairs was determined.
We find a strong over-representation of homologous enzymes at MPL 1.
We show that the functionally similar and functionally undetermined enzyme pairs are responsible for most of the over-representation of homologous enzyme pairs at MPL 1.

ConclusionsThe retrograde evolution model predicts that homologous enzymes pairs are at short metabolic distances from each other.
In general agreement with previous studies we find that homologous enzymes occur close to each other in the network more often than expected by chance, which lends some support to the retrograde evolution model.
However, we show that the homologous enzyme pairs which may have evolved through retrograde evolution, namely the pairs that are functionally dissimilar, show a weaker over-representation at MPL 1 than the functionally similar enzyme pairs.
Our study indicates that, while the retrograde evolution model may have played a small part, the patchwork evolution model is the predominant process of metabolic enzyme evolution.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-5-15 contains supplementary material, which is available to authorized users.

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Author: Sara Light - Per Kraulis

Source: https://link.springer.com/



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