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Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.

Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ, Charusanti P - Front Microbiol (2015)

Bottom Line: Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA.Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100-200 μM individual concentrations.These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University Cairo, Egypt ; Department of Bioengineering, University of California, San Diego La Jolla, CA, USA.

ABSTRACT
Mathematical models of biochemical networks form a cornerstone of bacterial systems biology. Inconsistencies between simulation output and experimental data point to gaps in knowledge about the fundamental biology of the organism. One such inconsistency centers on the gene aldA in Escherichia coli: it is essential in a computational model of E. coli metabolism, but experimentally it is not. Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA. Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100-200 μM individual concentrations. These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics.

No MeSH data available.


Related in: MedlinePlus

The model-predicted essential pathway catalyzed by AldA. Glycolaldehyde is a by-product of the essential tetrahydrofolate synthesis pathway in Escherichia coli. It is produced by dihydroneopterin aldolase, encoded by the gene folB. The aldA gene encodes glycolaldehyde dehydrogenase, which oxidizes glycolaldehyde to glycolate. In an ΔaldA knockout strain, the E. coli metabolic model predicts that glycolaldehyde will accumulate in the cell, leading to cell death (Orth et al., 2011). Experimentally, however, ΔaldA mutants are viable.
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Figure 1: The model-predicted essential pathway catalyzed by AldA. Glycolaldehyde is a by-product of the essential tetrahydrofolate synthesis pathway in Escherichia coli. It is produced by dihydroneopterin aldolase, encoded by the gene folB. The aldA gene encodes glycolaldehyde dehydrogenase, which oxidizes glycolaldehyde to glycolate. In an ΔaldA knockout strain, the E. coli metabolic model predicts that glycolaldehyde will accumulate in the cell, leading to cell death (Orth et al., 2011). Experimentally, however, ΔaldA mutants are viable.

Mentions: Simulations using the most recent version of the E. coli metabolic model (Orth et al., 2011) suggest that aldA should be an essential gene in glucose M9 media; however, the ΔaldA mutant is viable experimentally in this medium (Supplementary Figure S1). Glycolaldehyde dehydrogenase A (AldA), encoded by aldA, is an enzyme of broad specificity for small α-hydroxyaldehyde substrates (Baldoma and Aguilar, 1987). It is known to oxidize L-lactaldehyde to L-lactate in the metabolic pathways for L-fucose and L-rhamnose utilization, and catalyzes glycolaldehyde dehydrogenation of different pentoses such as D-arabinose and L-lyxose (LeBlanc and Mortlock, 1971; Badia et al., 1991). This latter function (and its encoding gene aldA) is predicted by the model to be essential for growth in glucose M9 because of its role in the folate biosynthesis pathway. In order for the model to synthesize folate, an essential metabolite, dihydroneopterin aldolase (FolB) must convert dihydroneopterin to 6-hydroxymethyl dihydropterin, which produces glycolaldehyde as a by-product. AldA then converts glycolaldehyde to glycolate (Figure 1). Without this reaction, an infinite amount of glycolaldehyde would accumulate in the model, which is an infeasible solution because it violates mass balance. Biologically, aldehydes are electrophilic compounds that are often toxic. Therefore accumulation of glycolaldehyde during the synthesis of folate due to an aldA gene disruption could be lethal to growth of E. coli. The E. coli ΔaldA mutant is viable in glucose M9, however, suggesting that either glycolaldehyde diffuses out through the membrane or is converted to glycolate by a different enzyme.


Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.

Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ, Charusanti P - Front Microbiol (2015)

The model-predicted essential pathway catalyzed by AldA. Glycolaldehyde is a by-product of the essential tetrahydrofolate synthesis pathway in Escherichia coli. It is produced by dihydroneopterin aldolase, encoded by the gene folB. The aldA gene encodes glycolaldehyde dehydrogenase, which oxidizes glycolaldehyde to glycolate. In an ΔaldA knockout strain, the E. coli metabolic model predicts that glycolaldehyde will accumulate in the cell, leading to cell death (Orth et al., 2011). Experimentally, however, ΔaldA mutants are viable.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585216&req=5

Figure 1: The model-predicted essential pathway catalyzed by AldA. Glycolaldehyde is a by-product of the essential tetrahydrofolate synthesis pathway in Escherichia coli. It is produced by dihydroneopterin aldolase, encoded by the gene folB. The aldA gene encodes glycolaldehyde dehydrogenase, which oxidizes glycolaldehyde to glycolate. In an ΔaldA knockout strain, the E. coli metabolic model predicts that glycolaldehyde will accumulate in the cell, leading to cell death (Orth et al., 2011). Experimentally, however, ΔaldA mutants are viable.
Mentions: Simulations using the most recent version of the E. coli metabolic model (Orth et al., 2011) suggest that aldA should be an essential gene in glucose M9 media; however, the ΔaldA mutant is viable experimentally in this medium (Supplementary Figure S1). Glycolaldehyde dehydrogenase A (AldA), encoded by aldA, is an enzyme of broad specificity for small α-hydroxyaldehyde substrates (Baldoma and Aguilar, 1987). It is known to oxidize L-lactaldehyde to L-lactate in the metabolic pathways for L-fucose and L-rhamnose utilization, and catalyzes glycolaldehyde dehydrogenation of different pentoses such as D-arabinose and L-lyxose (LeBlanc and Mortlock, 1971; Badia et al., 1991). This latter function (and its encoding gene aldA) is predicted by the model to be essential for growth in glucose M9 because of its role in the folate biosynthesis pathway. In order for the model to synthesize folate, an essential metabolite, dihydroneopterin aldolase (FolB) must convert dihydroneopterin to 6-hydroxymethyl dihydropterin, which produces glycolaldehyde as a by-product. AldA then converts glycolaldehyde to glycolate (Figure 1). Without this reaction, an infinite amount of glycolaldehyde would accumulate in the model, which is an infeasible solution because it violates mass balance. Biologically, aldehydes are electrophilic compounds that are often toxic. Therefore accumulation of glycolaldehyde during the synthesis of folate due to an aldA gene disruption could be lethal to growth of E. coli. The E. coli ΔaldA mutant is viable in glucose M9, however, suggesting that either glycolaldehyde diffuses out through the membrane or is converted to glycolate by a different enzyme.

Bottom Line: Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA.Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100-200 μM individual concentrations.These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University Cairo, Egypt ; Department of Bioengineering, University of California, San Diego La Jolla, CA, USA.

ABSTRACT
Mathematical models of biochemical networks form a cornerstone of bacterial systems biology. Inconsistencies between simulation output and experimental data point to gaps in knowledge about the fundamental biology of the organism. One such inconsistency centers on the gene aldA in Escherichia coli: it is essential in a computational model of E. coli metabolism, but experimentally it is not. Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA. Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100-200 μM individual concentrations. These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics.

No MeSH data available.


Related in: MedlinePlus