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Pareto optimal metabolic engineering for the growth-coupled overproduction of sustainable chemicals

Amaradio, M. N., Ojha, V. ORCID: https://orcid.org/0000-0002-9256-1192, Jansen, G., Gulisano, M., Costanza, J. and Nicosia, G. (2022) Pareto optimal metabolic engineering for the growth-coupled overproduction of sustainable chemicals. Biotechnology and Bioengineering. ISSN 0006-3592 (In Press)

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To link to this item DOI: 10.1002/bit.28103

Abstract/Summary

Our research aims to help industrial biotechnology develop a sustainable economy using green technology based on microorganisms and synthetic biology through two case studies that improve metabolic capacity in yeast models Yarrowia lipolytica (Y. lipolytica) and Saccharomyces cerevisiae (S. cerevisiae). We aim to increase the production capacity of beta-carotene (β-carotene) and succinic acid, which are among the highest market demands due to their versatile use in numerous consumer products. We performed simulations to identify in silico ranking of strains based on multiple objectives: the growth rate of yeast microorganisms, the number of used chromosomes, and the production capability of β-carotene (for Y. lipolytica) and succinate (for S. cerevisiae). Our multiobjective optimization methodology identified notable gene deletions by searching a vast solution-space to highlight near-optimal strains on Pareto Fronts, balancing the above-cited three objectives. Moreover, preserving the metabolic constraints and the essential genes, this work produced robust results: 7 significant strains of Y. lipolytica and 7 strains for S. cerevisiae. We examined gene knockout to study the function of genes and pathways. In fact, by studying the frequently silenced genes, we found that when the GPH1 gene is knocked out in S. cerevisiae, the isocitrate lyase enzyme is activated, which converts the isocitrate into succinate. Our goals are to simplify and facilitate the in vitro processes. Hence, we present strains with the least possible number of knockout genes and solutions in which the genes are turned off on the same chromosome. Therefore, we present results where the constraints mentioned above are met, like the strains where only two genes are switched off and other strains where half of the knockout genes are on the same chromosome. This research offers solutions for developing an efficient in vitro mutagenesis for microorganisms and demonstrates the efficiency of multiobjective optimization in automatizing metabolic engineering processes.

Item Type:Article
Refereed:Yes
Divisions:Science > School of Mathematical, Physical and Computational Sciences > Department of Computer Science
ID Code:104625
Publisher:Wiley

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