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

Abstract

Streptomyces clavuligerus (S. clavuligerus) has been widely studied for its ability to produce clavulanic acid (CA), a potent inhibitor of β-lactamase enzymes. In this study, S. clavuligerus cultivated in 2D rocking bioreactor in fed-batch operation produced CA at comparable rates to those observed in stirred tank bioreactors. A reduced model of S. clavuligerus metabolism was constructed by using a bottom-up approach and validated using experimental data. The reduced model was implemented for in silico studies of the metabolic scenarios arisen during the cultivations. Constraint-based analysis confirmed the interrelations between succinate, oxaloacetate, malate, pyruvate, and acetate accumulations at high CA synthesis rates in submerged cultures of S. clavuligerus. Further analysis using shadow prices provided a first view of the metabolites positive and negatively associated with the scenarios of low and high CA production.

Systems metabolic engineering of Streptomyces venezuelae for the enhanced production of pikromycin

“…In this study, we metabolically engineered S. venezuelae ATCC 15439 for the enhanced pikromycin production on the basis of gene manipulation targets predicted using its genome‐scale metabolic model (GEM). GEMs are a computational model that contains metabolic gene–protein‐reaction (GPR) associations at a genome‐scale, and can be simulated to predict metabolic flux distributions under a specific condition, which has demonstrated to be useful for systems metabolic engineering (Gu et al, 2019), including the production of secondary metabolites (Kim et al, 2016; Kittikunapong et al, 2021; Ramirez‐Malule et al, 2021). A GEM of S. venezuelae was newly reconstructed in this study, and used to predict overexpression and downregulation targets to improve the pikromycin production using S. venezuelae .…”

Heterologous overproduction of oviedomycin by refactoring biosynthetic gene cluster and metabolic engineering of host strain Streptomyces coelicolor

“…Metabolic engineering of host strains using genome-scale metabolic model (GEM) has been suggested as a promising strategy to improve the secondary metabolite production [ 25 , 26 ]. The GEM is a computational model that can predict metabolic flux distributions associated with the precursors of secondary metabolites under certain conditions, rendering it a valuable tool in the systems metabolic engineering [ 27 – 29 ]. Using GEM, it is possible to identify specific target genes for deletion and/or overexpression to enhance the production of desired secondary metabolites.…”

Dynamic in silico assessment of potential gene targets for enhancing clavulanic acid production in Streptomyces clavuligerus submerged cultures

“…The low CA productivity in the submerged cultivation of S. clavuligerus and the complexity of the downstream process have a direct impact on the production cost of this pharmaceutical compound, which is commonly coformulated with wide-spectrum β-lactam antibiotics. Strategies like nutritional and environmental perturbation appear as feasible alternatives to enhance the strain's productivity Ramirez-Malule, 2018). Metabolic engineering emerges as an alternative O n l i n e F i r s t for the rational enhancement of CA in S. clavuligerus cultures through the perturbation of metabolic and regulatory features (Liras and Martín, 2021).…”

“…In this sense, the systems biology approaches have contributed to the understanding of S. clavuligerus metabolism under different nutritional and environmental conditions (Gómez-Rios et al, 2022;Ramirez-Malule et al, 2021). Nevertheless, the classical steady-state approaches like the flux balance analysis (FBA) present limitations like the prediction of cellular growth and product secretion rates only for fixed values of substrate uptake rates.…”