An enhanced genome-scale metabolic reconstruction of Streptomyces clavuligerus identifies novel strain improvement strategies
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In this work, we expanded and updated a genome-scale metabolic model of Streptomyces clavuligerus. The model includes 1021 genes and 1494 biochemical reactions; genome-reaction information was curated and new features related to clavam metabolism and to the biomass synthesis equation were incorporated. The model was validated using experimental data from the literature and simulations were performed to predict cellular growth and clavulanic acid biosynthesis. Flux balance analysis (FBA) showed that limiting concentrations of phosphate and an excess of ammonia accumulation are unfavorable for growth and clavulanic acid biosynthesis. The evaluation of different objective functions for FBA showed that maximization of ATP yields the best predictions for cellular behavior in continuous cultures, while the maximization of growth rate provides better predictions for batch cultures. Through gene essentiality analysis, 130 essential genes were found using a limited in silico media, while 100 essential genes were identified in amino acid-supplemented media. Finally, a strain design was carried out to identify candidate genes to be overexpressed or knocked out so as to maximize antibiotic biosynthesis. Interestingly, potential metabolic engineering targets, identified in this study, have not been tested experimentally.
KeywordsGenome-scale metabolic reconstruction Flux balance analysis Streptomyces clavuligerus Strain improvement Clavulanic acid
The authors thank Professor Marnix H. Medema and Mohammad Tauqeer Alam for providing the template for the Streptomyces clavuligerus model, and Professor Andrzej Kierzek for advice on the SurreyFBA platform . This work was supported by Departamento Administrativo de Ciencia, Tecnología e Innovación—COLCIENCIAS-Colombia (Grant no. 111566945929). L. Toro and L. Pinilla thank COLCIENCIAS-Colombia for scholarships. C. Avignone-Rossa was supported by Grant BB/L02683X/1 from the Biotechnology and Biological Sciences Research Council (BBSRC, United Kingdom).
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Conflict of interest
The authors declare that they have no conflict of interest.
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