Chance and necessity in the evolution of minimal metabolic networks

  title={Chance and necessity in the evolution of minimal metabolic networks},
  author={Csaba P{\'a}l and Bal{\'a}zs Papp and Martin J. Lercher and P{\'e}ter Csermely and Stephen G. Oliver and Laurence D. Hurst},
It is possible to infer aspects of an organism's lifestyle from its gene content. Can the reverse also be done? Here we consider this issue by modelling evolution of the reduced genomes of endosymbiotic bacteria. The diversity of gene content in these bacteria may reflect both variation in selective forces and contingency-dependent loss of alternative pathways. Using an in silico representation of the metabolic network of Escherichia coli, we examine the role of contingency by repeatedly… 
Metabolic modeling of endosymbiont genome reduction on a temporal scale
While the timing of gene loss might be expected to be a completely stochastic evolutionary process, remarkably, it is found that metabolic considerations make a marked 40% contribution to determining when such losses occur.
Superessential reactions in metabolic networks
The metabolic genotype of an organism can change through loss and acquisition of enzyme-coding genes, while preserving its ability to survive and synthesize biomass in specific environments. This
Evolution of Metabolic Networks
A simple stochastic model of the evolutionary process of metabolic networks is introduced and the likelihood of the phylogeny of metabolisms is calculated to infer important parameters, such as the rates of creation and deletion of interactions between the metabolites.
Metabolic Networks of Sodalis glossinidius: A Systems Biology Approach to Reductive Evolution
Stoichiometric analysis reveals few gene inactivation events whose effects on the functionality of S. glossinidius metabolic systems are drastic enough to account for the ecological transition from a free-living to host-dependent lifestyle.
Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms
It is found that for all but the simplest metabolisms, most viable metabolisms can be transformed into one another by single viability-preserving reaction changes and historical contingency does not strongly restrict the origin of novel metabolic phenotypes.
Erosion of interaction networks in reduced and degraded genomes.
By inferring the PPIs present in the ancestor to contemporary Gammaproteobacteria, this work was able to trace the changes in gene repertoires, and their consequences on PPI network evolution, in several bacterial lineages that have independently undergone reductions in genome size and genome contents.
Environmental variability and modularity of bacterial metabolic networks
This study studies the relation between environmental variability and modularity in a natural and well-studied system, the metabolic networks of bacteria to find that metabolic Networks of organisms in variable environments are significantly more modular than networks of organisms that evolved under more constant conditions.
Metabolic adaptation after whole genome duplication.
The model confirms the hypothesis that W GD has been important in the adaptation of yeast to the new, glucose-rich environment that arose after the appearance of angiosperms and shows that WGD leads to better adaptation than small-scale duplications, in environments for which duplication of a whole pathway instead of single reactions is needed to increase fitness.
A critical view of metabolic network adaptations
It is concluded that the global topological characteristics of metabolic networks and their mutational robustness are unlikely to be directly shaped by natural selection, but various aspects of individual pathways and the behavior of the whole network show signs of adaptations, even though the exact selective forces often remain elusive.
Evolutionary constraints permeate large metabolic networks
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.


Computational inference of scenarios for alpha-proteobacterial genome evolution.
This study uses computational approaches to infer ancestral gene sets and to quantify the flux of genes along the branches of the alpha-proteobacterial species tree to reveal massive gene expansions at branches diversifying plant-associated bacteria and extreme losses at branches separating intracellular bacteria of animals and humans.
Determination of the Core of a Minimal Bacterial Gene Set
A computational comparative analysis of eight bacterial genomes was performed, and the proposed minimal genome contains 206 protein-coding genes with all the genetic information necessary for self-maintenance and reproduction in the presence of a full complement of essential nutrients and in the absence of environmental stress.
Community structure and metabolism through reconstruction of microbial genomes from the environment
Reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II and analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.
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This work reconstructs the gene content of ancestral Archaea and Proteobacteria and quantify the processes connecting them to their present day representatives based on the distribution of genes in completely sequenced genomes.
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It is shown that genome engineering is a feasible strategy for functional analysis of large gene clusters, and that removal of dispensable genomic regions may pave the way toward an optimized Bacillus cell factory.
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This work has shown that a constraint-based reconstruction and analysis approach provides a biochemically and genetically consistent framework for the generation of hypotheses and the testing of functions of microbial cells.
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  • J. Edwards, B. Palsson
  • Biology, Engineering
    Proceedings of the National Academy of Sciences of the United States of America
  • 2000
It was shown that based on stoichiometric and capacity constraints the in silico analysis was able to qualitatively predict the growth potential of mutant strains in 86% of the cases examined.
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
The notion that gene loss and HGT are major aspects of prokaryotic evolution was supported by quantitative analysis of the mapping of the phyletic patterns of COGs onto a hypothetical species tree.
Minimal Reaction Sets for Escherichia coli Metabolism under Different Growth Requirements and Uptake Environments
It is found that minimal reaction network sets are highly dependent on the uptake environment and the growth requirements imposed on the network, and it is predicted that the E. coli network, as described by the flux balance model, requires 224 metabolic reactions to support growth on a glucose‐ only medium and 229 for an acetate‐only medium, while only 122 reactions enable growth on an specially engineered growth medium.