Reductive evolution simulation

General concept

Gene content of organism undergoing genome reduction can be partially predicted if the environmental conditions of the organism and the gene content of an ancestor are known. The gene content of a genome-reduced organism is obtained by starting with a genome-scale model of a related organism with a larger genome. The media conditions and biomass function is modified to represent the environmental conditions and biomass composition of the reduced genome organism. Genes are subsequently removed if FBA predicts a biomass greater than a specified threshold. This is repeated until no additional genes can be removed. Since this provides only a candidate gene set, this process is repeated to assess the entire range of possible gene sets.

Items to consider when implementing

Software packages with this method

Applications of interest

Pal, et al. (2006) demonstrated that the minimal set of genes from reductive evolution simulation is consistent with the genes retained in the reduced Buchnera aphidicola genome.

Yizhak, et al. (2011) showed that the order of gene loss predicted by reductive evolution simulation correlates with the order of gene loss among Buchnera genomes.

Belda, et al. (2012) simulated genome reduction in Sodalis glossinidius, an endosymbiont of tsetse flies that is believed to be in the early stages of genome reduction.

Relevant references

Pál C, Papp B, Lercher MJ, Csermely P, Oliver SG, Hurst LD. Chance and necessity in the evolution of minimal metabolic networks. Nature. 2006 Mar 30;440(7084):667-70.

Yizhak K, Tuller T, Papp B, Ruppin E. Metabolic modeling of endosymbiont genome reduction on a temporal scale. Mol Syst Biol. 2011 Mar 29;7:479.

Belda E, Silva FJ, Peretó J, Moya A. Metabolic Networks of Sodalis glossinidius: A Systems Biology Approach to Reductive Evolution. PLoS One. 2012;7(1):e30652.

Related methods

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