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.

Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks

Flux balance analysis studies a vast space of metabolic network genotypes and their relationship to metabolic phenotypes, the ability to sustain life in an environment defined by an available spectrum of carbon sources, to suggest that the robustness of the Escherichia coli metabolic network to mutations is typical of networks with the same phenotype.

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.

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

A computational framework for analyzing and interpreting pan-reactomes that provides novel insights into the ecological and evolutionary drivers of pan-genome dynamics is introduced.

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.

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.



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.

Genomes in flux: the evolution of archaeal and proteobacterial gene content.

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.

Genome engineering reveals large dispensable regions in Bacillus subtilis.

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.

Genome-scale models of microbial cells: evaluating the consequences of constraints

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.

The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.

  • J. EdwardsB. 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.

Bacterial genome size reduction by experimental evolution.

The results suggest that extensive genome reduction can occur on a short evolutionary time scale and that RecA-dependent homologous recombination only plays a limited role in this process of jettisoning superfluous DNA.

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.