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Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data
BackgroundGenome-scale metabolic models (GEMs) serve as effective tools for understanding cellular phenotypes and predicting engineering targets in...
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Reconstruction of a genome-scale metabolic model and in-silico flux analysis of Aspergillus tubingensis: a non-mycotoxinogenic citric acid-producing fungus
BackgroundAspergillus tubingensis is a citric acid-producing fungus that can utilize sugars in hydrolysate of lignocellulosic biomass such as...
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Genome-scale metabolic model analysis of Pichia pastoris for enhancing the production of S-adenosyl-l-methionine
Komagataella phaffii , formerly Pichia pastoris ( P. pastoris ), is a promising methylotrophic yeast used in industry to produce recombinant protein and...
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Metabolic engineering of Bacillus subtilis based on genome-scale metabolic model to promote fengycin production
Fengycin is an important lipopeptide antibiotic that can be produced by Bacillus subtilis . However, the production capacity of the unmodified wild...
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Metabolic Engineering of Lipid Biosynthesis Pathway to Enhance the Oil Content in Microalgae
Today, a large range of software programmes are used in the field of metabolic engineering. Such applications were shaped to provide support for a...
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Reconstruction of Genome-Scale Metabolic Model for Hansenula polymorpha Using RAVEN
Genome-scale metabolic models (GEMs) provide a useful framework for modeling the metabolism of microorganisms. While the applications of GEMs are...
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Improvement of Lutein Production in Auxenochlorella protothecoides Using Its Genome-Scale Metabolic Model and a System-Oriented Approach
Lutein is a valuable metabolite widely used in the food, pharmaceutical, cosmetic, and aquaculture industries. Marigold flowers are the most common...
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Microbial Isoprenoid Production: An Example of Green Chemistry through Metabolic Engineering
Saving energy, cost efficiency, producing less waste, improving the biodegradability of products, potential for producing novel and complex...
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Integration of Aspergillus niger transcriptomic profile with metabolic model identifies potential targets to optimise citric acid production from lignocellulosic hydrolysate
BackgroundCitric acid is typically produced industrially by Aspergillus niger -mediated fermentation of a sucrose-based feedstock, such as molasses....
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Reconstruction of genome-scale metabolic models of non-conventional yeasts: current state, challenges, and perspectives
Non-conventional yeasts are promising cell factories to produce lipids and oleochemicals, metabolites of industrial interest ( e.g ., organics acids,...
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Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions
BackgroundGenome-scale metabolic model (GSMM) is a powerful tool for the study of cellular metabolic characteristics. With the development of...
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Systematizing Microbial Bioplastic Production for Develo** Sustainable Bioeconomy: Metabolic Nexus Modeling, Economic and Environmental Technologies Assessment
The excessive usage of non-renewable resources to produce plastic commodities has incongruously influenced the environment’s health. Especially in...
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Improved production of Taxol® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering
BackgroundIntegrated metabolic engineering approaches that combine system and synthetic biology tools enable the efficient design of microbial cell...
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A new strategy for dynamic metabolic flux estimation by integrating transient metabolome data into genome-scale metabolic models
Metabolic flux analysis (MFA) is a powerful tool for studying microbial cell physiology. Isotope-based MFA is the accepted standard for studying...
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Metabolic flux sampling predicts strain-dependent differences related to aroma production among commercial wine yeasts
BackgroundMetabolomics coupled with genome-scale metabolic modeling approaches have been employed recently to quantitatively analyze the...
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In silico-guided metabolic engineering of Bacillus subtilis for efficient biosynthesis of purine nucleosides by blocking the key backflow nodes
BackgroundPurine nucleosides play essential roles in cellular physiological processes and have a wide range of applications in the fields of...
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Multivariate modular metabolic engineering for enhanced l-methionine biosynthesis in Escherichia coli
Backgroundl -Methionine is the only bulk amino acid that has not been industrially produced by the fermentation method. Due to highly complex and...
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Comprehensive network of stress-induced responses in Zymomonas mobilis during bioethanol production: from physiological and molecular responses to the effects of system metabolic engineering
Nowadays, biofuels, especially bioethanol, are becoming increasingly popular as an alternative to fossil fuels. Zymomonas mobilis is a desirable...
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Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction
Enzyme turnover numbers ( k cat ) are key to understanding cellular metabolism, proteome allocation and physiological diversity, but experimentally...
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Mechanistic Model-Driven Biodesign in Mammalian Synthetic Biology
Mathematical modeling plays a vital role in mammalian synthetic biology by providing a framework to design and optimize design circuits and...