Use of genome-scale metabolic models in evolutionary systems biology

B. Papp, Balázs Szappanos, Richard A. Notebaart

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Citations (Scopus)

Abstract

One of the major aims of the nascent field of evolutionary systems biology is to test evolutionary hypotheses that are not only realistic from a population genetic point of view but also detailed in terms of molecular biology mechanisms. By providing a mapping between genotype and phenotype for hundreds of genes, genome-scale systems biology models of metabolic networks have already provided valuable insights into the evolution of metabolic gene contents and phenotypes of yeast and other microbial species. Here we review the recent use of these computational models to predict the fitness effect of mutations, genetic interactions, evolutionary outcomes, and to decipher the mechanisms of mutational robustness. While these studies have demonstrated that even simplified models of biochemical reaction networks can be highly informative for evolutionary analyses, they have also revealed the weakness of this modeling framework to quantitatively predict mutational effects, a challenge that needs to be addressed for future progress in evolutionary systems biology.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
Pages483-497
Number of pages15
Volume759
DOIs
Publication statusPublished - 2011

Publication series

NameMethods in Molecular Biology
Volume759
ISSN (Print)10643745

Fingerprint

Systems Biology
Genome
Phenotype
Population Genetics
Metabolic Networks and Pathways
Genes
Molecular Biology
Yeasts
Genotype
Mutation

Keywords

  • constraint-based modeling
  • fitness landscape
  • Flux balance analysis (FBA)
  • gene essentiality
  • genetic interaction
  • genome evolution
  • metabolic network
  • Saccharomyces cerevisiae

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Papp, B., Szappanos, B., & Notebaart, R. A. (2011). Use of genome-scale metabolic models in evolutionary systems biology. In Methods in Molecular Biology (Vol. 759, pp. 483-497). (Methods in Molecular Biology; Vol. 759). https://doi.org/10.1007/978-1-61779-173-4_27

Use of genome-scale metabolic models in evolutionary systems biology. / Papp, B.; Szappanos, Balázs; Notebaart, Richard A.

Methods in Molecular Biology. Vol. 759 2011. p. 483-497 (Methods in Molecular Biology; Vol. 759).

Research output: Chapter in Book/Report/Conference proceedingChapter

Papp, B, Szappanos, B & Notebaart, RA 2011, Use of genome-scale metabolic models in evolutionary systems biology. in Methods in Molecular Biology. vol. 759, Methods in Molecular Biology, vol. 759, pp. 483-497. https://doi.org/10.1007/978-1-61779-173-4_27
Papp B, Szappanos B, Notebaart RA. Use of genome-scale metabolic models in evolutionary systems biology. In Methods in Molecular Biology. Vol. 759. 2011. p. 483-497. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-61779-173-4_27
Papp, B. ; Szappanos, Balázs ; Notebaart, Richard A. / Use of genome-scale metabolic models in evolutionary systems biology. Methods in Molecular Biology. Vol. 759 2011. pp. 483-497 (Methods in Molecular Biology).
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