Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism

Abstract

Streptomyces are filamentous soil bacteria that produce more than half of the known microbial antibiotics. We present the first genome-scale metabolic model of a representative of this group--Streptomyces coelicolor A3(2). The metabolism reconstruction was based on annotated genes, physiological and biochemical information. The stoichiometric model includes 819 biochemical conversions and 152 transport reactions, accounting for a total of 971 reactions. Of the reactions in the network, 700 are unique, while the rest are iso-reactions. The network comprises 500 metabolites. A total of 711 open reading frames (ORFs) were included in the model, which corresponds to 13% of the ORFs with assigned function in the S. coelicolor A3(2) genome. In a comparative analysis with the Streptomyces avermitilis genome, we showed that the metabolic genes are highly conserved between these species and therefore the model is suitable for use with other Streptomycetes. Flux balance analysis was applied for studies of the reconstructed metabolic network and to assess its metabolic capabilities for growth and polyketides production. The model predictions of wild-type and mutants' growth on different carbon and nitrogen sources agreed with the experimental data in most cases. We estimated the impact of each reaction knockout on the growth of the in silico strain on 62 carbon sources and two nitrogen sources, thereby identifying the "core" of the essential reactions. We also illustrated how reconstruction of a metabolic network at the genome level can be used to fill gaps in genome annotation.

Figure 1.

Frequency of the most connected metabolites in the reconstructed metabolic networks of S. coelicolor A3(2), S. cerevisiae (Förster et al. 2003a), and E. coli (Edwards and Palsson 2000b). Frequency is calculated as the number of times a certain metabolite appears in the metabolic network divided by the sum of all metabolite occurrences. S. coelicolor A3(2) (•), S. cerevisiae (▵), E. coli (□). (H) External proton; (GLU) glutamate; (PPI) pyrophosphate; (COA) coenzyme A; (AKG) α-ketoglutarate; (PYR) pyruvate; (ACCOA) acetyl-coenzyme A; (ACP) acetyl-carrier protein.

Figure 2.

The ATP yield coefficient Y_xATP (○) and maintenance energy m_ATP (▪) as a function of the maximal P/O ratio in S. coelicolor A3(2).

Figure 3.

Simulation of experimental chemostates data (Melzoch et al. 1997). Specific glucose uptake rate (experimental ▴, model ----), specific carbon dioxide production rate (experimental ♦, model ―), specific oxygen uptake rate (experimental □, model ---), and actinorhodin production rate (experimental ○, model — - — - — -).

Figure 4.

Activity of the reactions in the model of S. coelicolor A3(2). All the unique reactions in the model are divided into several categories based on their predicted activity under different growth conditions. The proportion of reactions for which the corresponding enzymes were detected on a 2D gel is shown by the dashed areas.

Figure 5.

Essentiality of the reactions in the model of S. coelicolor A3(2) during growth on glucose (A) and during growth under 63 various conditions (B). All the reactions were sorted into three categories: essential reactions, conditionally essential reactions, and nonessential reactions depending on their influence on biomass synthesis. The percentage of reactions with isoenzymes among all the reactions in the given category is shown.

Figure 6.

Maximal simulated biomass yield of S. coelicolor A3(2) as compared to (A) S. cerevisiae (Förster et al. 2003a) and (B) E. coli (Edwards and Palsson 2000b) on different carbon sources (gram/gram substrate). All the calculations were made for substrate uptake rate of 6 C-mmol/g DW/h. The maintenance energy requirement was considered.

Figure 7.

Predicted polyketides production capabilities of S. coelicolor A3(2) and S. cerevisiae (Förster et al. 2003a) (in moles per mole glucose). All the calculations were made for the glucose uptake rate of 1 mmol/g DW/h.