Metabolic modeling of endosymbiont genome reduction on a temporal scale

Keren Yizhak, Tamir Tuller, B. Papp, Eytan Ruppin

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

A fundamental challenge in Systems Biology is whether a cell-scale metabolic model can predict patterns of genome evolution by realistically accounting for associated biochemical constraints. Here, we study the order in which genes are lost in an in silico evolutionary process, leading from the metabolic network of Eschericia coli to that of the endosymbiont Buchnera aphidicola. We examine how this order correlates with the order by which the genes were actually lost, as estimated from a phylogenetic reconstruction. By optimizing this correlation across the space of potential growth and biomass conditions, we compute an upper bound estimate on the model's prediction accuracy (R=0.54). The model's network-based predictive ability outperforms predictions obtained using genomic features of individual genes, reflecting the effect of selection imposed by metabolic stoichiometric constraints. Thus, while the timing of gene loss might be expected to be a completely stochastic evolutionary process, remarkably, we find that metabolic considerations, on their own, make a marked 40% contribution to determining when such losses occur.

Original languageEnglish
Article number479
JournalMolecular systems biology [electronic resource].
Volume7
DOIs
Publication statusPublished - 2011

Fingerprint

endosymbionts
Genome
Genes
Gene
genome
Buchnera
Modeling
Stochastic Processes
Gene Order
Systems Biology
genes
Buchnera aphidicola
Metabolic Networks and Pathways
Computer Simulation
Biomass
prediction
Metabolic Network
Phylogenetics
Prediction Model
Correlate

Keywords

  • constraint-based modeling
  • endosymbiont
  • evolution
  • metabolism

ASJC Scopus subject areas

  • Medicine(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Computational Theory and Mathematics
  • Information Systems
  • Applied Mathematics

Cite this

Metabolic modeling of endosymbiont genome reduction on a temporal scale. / Yizhak, Keren; Tuller, Tamir; Papp, B.; Ruppin, Eytan.

In: Molecular systems biology [electronic resource]., Vol. 7, 479, 2011.

Research output: Contribution to journalArticle

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