Data set of in silico simulation for the production of clavulanic acid and cephamycin C by Streptomyces clavuligerus using a genome scale metabolic model

Abstract

Streptomyces clavuligerus ( S. clavuligerus ) is a Gram-positive bacterium which produced clavulanic acid (CA) and cephamycin C (CephC). In this data article, a curated genome scale metabolic model of S. clavuligerus is presented. A total of eighteen objective functions were evaluated for a better representation of CA and CephC production by S. clavuligerus . The different objective functions were evaluated varying the weighting factors of CA and CephC between 0, 1 y 2, whereas for the case of biomass the weight factor was varied between 1 and 2. A robustness analysis, by mean of flux balance analysis, showed five different metabolic phenotypes of S. clavuligerus as a function of oxygen uptake: (I) and (II) biomass production, (III) biomass and CephC production, (IV) simultaneous production of biomass, CA and CephC and (V) production of biomass and CA. Data of shadow prices and reduced cost are also presented.

A Genome-Scale Insight into the Effect of Shear Stress During the Fed-Batch Production of Clavulanic Acid by Streptomyces Clavuligerus

“…A common approach for studying the effect of nutritional, genetic and environmental perturbations on metabolism is the genome-scale metabolic modeling using flux balance analysis (FBA) [ 21 ]. In the case of S. clavuligerus , metabolic network models have been reconstructed and/or updated for this purpose [ 10 , 22 , 23 , 24 ], providing insights about the metabolic features of the species and possible genetic targets for further strain improvement. Nevertheless, the referred models share a common origin and some of their inconsistencies persisted between them without being corrected.…”

Clavulanic Acid Production by Streptomyces clavuligerus: Insights from Systems Biology, Strain Engineering, and Downstream Processing

“…Application and use of genome-scale metabolic modeling of Streptomyces bacteria is currently an active field of study [ 138 , 145 , 162 , 163 , 164 ], including the modeling of S. clavuligerus metabolism ( Figure 4 ) [ 19 , 43 , 122 , 165 , 166 ].…”

“…The last model was updated and curated in 2019, containing 1534 reactions, 1199 metabolites and 871 genes [ 166 ]. Although this model was not validated with experimental data, it explored 18 objective functions and metabolic phenotypes of S. clavuligerus during production of CA and Cephamycin C.…”

TCA Cycle and Its Relationship with Clavulanic Acid Production: A Further Interpretation by Using a Reduced Genome-Scale Metabolic Model of Streptomyces clavuligerus

“…GEMs work under the optimization of a cellular objective (usually the maximization of the biomass growth rate) with the aim of predicting carbon flux distributions [ 26 ]. Five GEMs have been published and used as tools for assessing the complexity of S. clavuligerus metabolism in silico, especially in connection with antibiotics production (CA and cephamycin C) [ 20 , 21 , 27 , 28 , 29 ]. The previous stoichiometric metabolic models for S. clavuligerus were not reconstructed de novo from the organism-specific reference sequences; instead, rather new biochemical information was added to the first GEM without changing its initial structure [ 9 , 21 ].…”