Metabolic Determinants of Enzyme Evolution in a Genome-Scale Bacterial Metabolic Network

Overview

Journal Genome Biol Evol

Publisher Oxford University Press

Specialties Biology
Genetics
Molecular Biology

Date 2018 Oct 24

PMID 30351420

Citations 13

Authors

Jose Aguilar-Rodriguez

Andreas Wagner

Affiliations

Soon will be listed here.

Abstract

Different genes and proteins evolve at very different rates. To identify the factors that explain these differences is an important aspect of research in molecular evolution. One such factor is the role a protein plays in a large molecular network. Here, we analyze the evolutionary rates of enzyme-coding genes in the genome-scale metabolic network of Escherichia coli to find the evolutionary constraints imposed by the structure and function of this complex metabolic system. Central and highly connected enzymes appear to evolve more slowly than less connected enzymes, but we find that they do so as a by-product of their high abundance, and not because of their position in the metabolic network. In contrast, enzymes catalyzing reactions with high metabolic flux-high substrate to product conversion rates-evolve slowly even after we account for their abundance. Moreover, enzymes catalyzing reactions that are difficult to by-pass through alternative pathways, such that they are essential in many different genetic backgrounds, also evolve more slowly. Our analyses show that an enzyme's role in the function of a metabolic network affects its evolution more than its place in the network's structure. They highlight the value of a system-level perspective for studies of molecular evolution.

Citing Articles

The Architecture of Metabolic Networks Constrains the Evolution of Microbial Resource Hierarchies.

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Functional comparison of metabolic networks across species.

Ramon C, Stelling J Nat Commun. 2023; 14(1):1699.

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The origin of genetic and metabolic systems: Evolutionary structuralinsights.

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Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes.

Garza D, von Meijenfeldt F, van Dijk B, Boleij A, Huynen M, Dutilh B BMC Ecol Evol. 2022; 22(1):101.

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The Influence of Codon Usage, Protein Abundance, and Protein Stability on Protein Evolution Vary by Evolutionary Distance and the Type of Protein.

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