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Predicting synthetic rescues in metabolic networks.

Motter AE, Gulbahce N, Almaas E, Barabási AL - Mol. Syst. Biol. (2008)

Bottom Line: Focusing on the metabolism of single-cell organisms, we computationally study mutants that lack an essential enzyme, and thus are unable to grow or have a significantly reduced growth rate.We show that several of these mutants can be turned into viable organisms through additional gene deletions that restore their growth rate.The systematic network-based identification of compensatory rescue effects may open new avenues for genetic interventions.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics and Astronomy and Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA. motter@northwestern.edu

ABSTRACT
An important goal of medical research is to develop methods to recover the loss of cellular function due to mutations and other defects. Many approaches based on gene therapy aim to repair the defective gene or to insert genes with compensatory function. Here, we propose an alternative, network-based strategy that aims to restore biological function by forcing the cell to either bypass the functions affected by the defective gene, or to compensate for the lost function. Focusing on the metabolism of single-cell organisms, we computationally study mutants that lack an essential enzyme, and thus are unable to grow or have a significantly reduced growth rate. We show that several of these mutants can be turned into viable organisms through additional gene deletions that restore their growth rate. In a rather counterintuitive fashion, this is achieved via additional damage to the metabolic network. Using flux balance-based approaches, we identify a number of synthetically viable gene pairs, in which the removal of one enzyme-encoding gene results in a non-viable phenotype, while the deletion of a second enzyme-encoding gene rescues the organism. The systematic network-based identification of compensatory rescue effects may open new avenues for genetic interventions.

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The impact of rescue deletions for E. coli (A, B) and S. cerevisiae (C, D) gene-deficient mutants. (A, C) Predicted biomass production before (○) and after (•) rescue deletions in glucose minimal media. The mutants are generated through the deletion of the genes shown at the x-axis. We show the results for all mutants with G1MOMA<G1FBA such that G1MOMA≤0.8 GwtFBA and G1FBA≥0.2 GwtFBA. If the rescue deletion changes the growth rate from zero to some positive value, we observe the Lazarus effect, applying to suboptimally essential genes (left). If the rescue deletion only enhances the growth rate, we observe a suboptimal recovery (right). The experimental information on the lethality of the original E. coli (Edwards and Palsson, 2000; Gerdes et al, 2003; Baba et al, 2006; PEC, 2007) and S. cerevisiae (Giaever et al, 2002; Steinmetz et al, 2002; SDG, 2007) gene-deficient mutants is indicated with (+) for viable mutants, (−) for non-viable mutants, and (a) for a gene absent in the databases. (B, D) Same as in (A, C) for single-gene rescue deletions in various media. We show selected mutants with significant biomass improvements after the rescue deletion of a single gene. The rescue deletion is indicated at the top, and the tested media are indicated at the bottom. The abbreviations stand for acetate (Ac), α-ketoglutarate (Akg), arabinose (Ara), ethanol (Eth), galactose (Gal), glucose (Glc), glucose anaerobic (Glca), glycerol (Gly), lactate (Lac), malate (Mal), mannose (Man), pyruvate (Pyr), rich medium (Rich) (see Supplementary Information), sorbitol (Sor), succinate (Succ), sucrose (Suc), and xylose (Xyl). The biomass fluxes are normalized by the wild-type flux GwtFBA in all panels. In units of mmol/g DW-h, the wild-type fluxes for E. coli are 0.187 (Ac), 0.535 (Akg), 0.745 (Ara), 0.908 (Glc), 0.367 (Lac), 0.388 (Mal), 0.908 (Man), 0.303 (Pyr), 2.87 (Rich), 0.418 (Succ), and 1.37 (Suc), while for S. cerevisiae they are 0.189 (Ac), 0.311 (Eth), 0.703 (Gal), 0.819 (Glc), 0.180 (Glca), 0.532 (Gly), 1.34 (Rich), 0.798 (Sor), and 0.742 (Xyl). All the genes involved in the rescues of (A, C) are listed in Supplementary Information, while the minimum rescue sets are listed in Supplementary Tables SII and SIII, respectively. The alternative rescue genes for each media in (B, D) are listed along with the corresponding recoveries in Supplementary Information.
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f4: The impact of rescue deletions for E. coli (A, B) and S. cerevisiae (C, D) gene-deficient mutants. (A, C) Predicted biomass production before (○) and after (•) rescue deletions in glucose minimal media. The mutants are generated through the deletion of the genes shown at the x-axis. We show the results for all mutants with G1MOMA<G1FBA such that G1MOMA≤0.8 GwtFBA and G1FBA≥0.2 GwtFBA. If the rescue deletion changes the growth rate from zero to some positive value, we observe the Lazarus effect, applying to suboptimally essential genes (left). If the rescue deletion only enhances the growth rate, we observe a suboptimal recovery (right). The experimental information on the lethality of the original E. coli (Edwards and Palsson, 2000; Gerdes et al, 2003; Baba et al, 2006; PEC, 2007) and S. cerevisiae (Giaever et al, 2002; Steinmetz et al, 2002; SDG, 2007) gene-deficient mutants is indicated with (+) for viable mutants, (−) for non-viable mutants, and (a) for a gene absent in the databases. (B, D) Same as in (A, C) for single-gene rescue deletions in various media. We show selected mutants with significant biomass improvements after the rescue deletion of a single gene. The rescue deletion is indicated at the top, and the tested media are indicated at the bottom. The abbreviations stand for acetate (Ac), α-ketoglutarate (Akg), arabinose (Ara), ethanol (Eth), galactose (Gal), glucose (Glc), glucose anaerobic (Glca), glycerol (Gly), lactate (Lac), malate (Mal), mannose (Man), pyruvate (Pyr), rich medium (Rich) (see Supplementary Information), sorbitol (Sor), succinate (Succ), sucrose (Suc), and xylose (Xyl). The biomass fluxes are normalized by the wild-type flux GwtFBA in all panels. In units of mmol/g DW-h, the wild-type fluxes for E. coli are 0.187 (Ac), 0.535 (Akg), 0.745 (Ara), 0.908 (Glc), 0.367 (Lac), 0.388 (Mal), 0.908 (Man), 0.303 (Pyr), 2.87 (Rich), 0.418 (Succ), and 1.37 (Suc), while for S. cerevisiae they are 0.189 (Ac), 0.311 (Eth), 0.703 (Gal), 0.819 (Glc), 0.180 (Glca), 0.532 (Gly), 1.34 (Rich), 0.798 (Sor), and 0.742 (Xyl). All the genes involved in the rescues of (A, C) are listed in Supplementary Information, while the minimum rescue sets are listed in Supplementary Tables SII and SIII, respectively. The alternative rescue genes for each media in (B, D) are listed along with the corresponding recoveries in Supplementary Information.

Mentions: Systematically applying our method to the E. coli metabolism in glucose minimal medium, we identified 6 suboptimally essential genes, which represent candidates for the Lazarus effect, and 17 candidates for suboptimal recovery (see Figure 4A). Most of the mutants miss genes involved in the central metabolism, while a few miss genes that participate in amino-acid metabolism and transport processes. Of particular interest are mutants with the genes pfk, fbaA, or tpiA deleted, whose essentiality has been tested and is supported by experiments (Fraenkel, 1987). As we show in Supplementary Table SI and Figure 4A, the growth rate of these mutants is restored by additional targeted gene deletions that increase the suboptimal growth rate from zero to more than 45% of the wild-type growth rate.


Predicting synthetic rescues in metabolic networks.

Motter AE, Gulbahce N, Almaas E, Barabási AL - Mol. Syst. Biol. (2008)

The impact of rescue deletions for E. coli (A, B) and S. cerevisiae (C, D) gene-deficient mutants. (A, C) Predicted biomass production before (○) and after (•) rescue deletions in glucose minimal media. The mutants are generated through the deletion of the genes shown at the x-axis. We show the results for all mutants with G1MOMA<G1FBA such that G1MOMA≤0.8 GwtFBA and G1FBA≥0.2 GwtFBA. If the rescue deletion changes the growth rate from zero to some positive value, we observe the Lazarus effect, applying to suboptimally essential genes (left). If the rescue deletion only enhances the growth rate, we observe a suboptimal recovery (right). The experimental information on the lethality of the original E. coli (Edwards and Palsson, 2000; Gerdes et al, 2003; Baba et al, 2006; PEC, 2007) and S. cerevisiae (Giaever et al, 2002; Steinmetz et al, 2002; SDG, 2007) gene-deficient mutants is indicated with (+) for viable mutants, (−) for non-viable mutants, and (a) for a gene absent in the databases. (B, D) Same as in (A, C) for single-gene rescue deletions in various media. We show selected mutants with significant biomass improvements after the rescue deletion of a single gene. The rescue deletion is indicated at the top, and the tested media are indicated at the bottom. The abbreviations stand for acetate (Ac), α-ketoglutarate (Akg), arabinose (Ara), ethanol (Eth), galactose (Gal), glucose (Glc), glucose anaerobic (Glca), glycerol (Gly), lactate (Lac), malate (Mal), mannose (Man), pyruvate (Pyr), rich medium (Rich) (see Supplementary Information), sorbitol (Sor), succinate (Succ), sucrose (Suc), and xylose (Xyl). The biomass fluxes are normalized by the wild-type flux GwtFBA in all panels. In units of mmol/g DW-h, the wild-type fluxes for E. coli are 0.187 (Ac), 0.535 (Akg), 0.745 (Ara), 0.908 (Glc), 0.367 (Lac), 0.388 (Mal), 0.908 (Man), 0.303 (Pyr), 2.87 (Rich), 0.418 (Succ), and 1.37 (Suc), while for S. cerevisiae they are 0.189 (Ac), 0.311 (Eth), 0.703 (Gal), 0.819 (Glc), 0.180 (Glca), 0.532 (Gly), 1.34 (Rich), 0.798 (Sor), and 0.742 (Xyl). All the genes involved in the rescues of (A, C) are listed in Supplementary Information, while the minimum rescue sets are listed in Supplementary Tables SII and SIII, respectively. The alternative rescue genes for each media in (B, D) are listed along with the corresponding recoveries in Supplementary Information.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2267730&req=5

f4: The impact of rescue deletions for E. coli (A, B) and S. cerevisiae (C, D) gene-deficient mutants. (A, C) Predicted biomass production before (○) and after (•) rescue deletions in glucose minimal media. The mutants are generated through the deletion of the genes shown at the x-axis. We show the results for all mutants with G1MOMA<G1FBA such that G1MOMA≤0.8 GwtFBA and G1FBA≥0.2 GwtFBA. If the rescue deletion changes the growth rate from zero to some positive value, we observe the Lazarus effect, applying to suboptimally essential genes (left). If the rescue deletion only enhances the growth rate, we observe a suboptimal recovery (right). The experimental information on the lethality of the original E. coli (Edwards and Palsson, 2000; Gerdes et al, 2003; Baba et al, 2006; PEC, 2007) and S. cerevisiae (Giaever et al, 2002; Steinmetz et al, 2002; SDG, 2007) gene-deficient mutants is indicated with (+) for viable mutants, (−) for non-viable mutants, and (a) for a gene absent in the databases. (B, D) Same as in (A, C) for single-gene rescue deletions in various media. We show selected mutants with significant biomass improvements after the rescue deletion of a single gene. The rescue deletion is indicated at the top, and the tested media are indicated at the bottom. The abbreviations stand for acetate (Ac), α-ketoglutarate (Akg), arabinose (Ara), ethanol (Eth), galactose (Gal), glucose (Glc), glucose anaerobic (Glca), glycerol (Gly), lactate (Lac), malate (Mal), mannose (Man), pyruvate (Pyr), rich medium (Rich) (see Supplementary Information), sorbitol (Sor), succinate (Succ), sucrose (Suc), and xylose (Xyl). The biomass fluxes are normalized by the wild-type flux GwtFBA in all panels. In units of mmol/g DW-h, the wild-type fluxes for E. coli are 0.187 (Ac), 0.535 (Akg), 0.745 (Ara), 0.908 (Glc), 0.367 (Lac), 0.388 (Mal), 0.908 (Man), 0.303 (Pyr), 2.87 (Rich), 0.418 (Succ), and 1.37 (Suc), while for S. cerevisiae they are 0.189 (Ac), 0.311 (Eth), 0.703 (Gal), 0.819 (Glc), 0.180 (Glca), 0.532 (Gly), 1.34 (Rich), 0.798 (Sor), and 0.742 (Xyl). All the genes involved in the rescues of (A, C) are listed in Supplementary Information, while the minimum rescue sets are listed in Supplementary Tables SII and SIII, respectively. The alternative rescue genes for each media in (B, D) are listed along with the corresponding recoveries in Supplementary Information.
Mentions: Systematically applying our method to the E. coli metabolism in glucose minimal medium, we identified 6 suboptimally essential genes, which represent candidates for the Lazarus effect, and 17 candidates for suboptimal recovery (see Figure 4A). Most of the mutants miss genes involved in the central metabolism, while a few miss genes that participate in amino-acid metabolism and transport processes. Of particular interest are mutants with the genes pfk, fbaA, or tpiA deleted, whose essentiality has been tested and is supported by experiments (Fraenkel, 1987). As we show in Supplementary Table SI and Figure 4A, the growth rate of these mutants is restored by additional targeted gene deletions that increase the suboptimal growth rate from zero to more than 45% of the wild-type growth rate.

Bottom Line: Focusing on the metabolism of single-cell organisms, we computationally study mutants that lack an essential enzyme, and thus are unable to grow or have a significantly reduced growth rate.We show that several of these mutants can be turned into viable organisms through additional gene deletions that restore their growth rate.The systematic network-based identification of compensatory rescue effects may open new avenues for genetic interventions.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics and Astronomy and Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA. motter@northwestern.edu

ABSTRACT
An important goal of medical research is to develop methods to recover the loss of cellular function due to mutations and other defects. Many approaches based on gene therapy aim to repair the defective gene or to insert genes with compensatory function. Here, we propose an alternative, network-based strategy that aims to restore biological function by forcing the cell to either bypass the functions affected by the defective gene, or to compensate for the lost function. Focusing on the metabolism of single-cell organisms, we computationally study mutants that lack an essential enzyme, and thus are unable to grow or have a significantly reduced growth rate. We show that several of these mutants can be turned into viable organisms through additional gene deletions that restore their growth rate. In a rather counterintuitive fashion, this is achieved via additional damage to the metabolic network. Using flux balance-based approaches, we identify a number of synthetically viable gene pairs, in which the removal of one enzyme-encoding gene results in a non-viable phenotype, while the deletion of a second enzyme-encoding gene rescues the organism. The systematic network-based identification of compensatory rescue effects may open new avenues for genetic interventions.

Show MeSH
Related in: MedlinePlus