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Na D.,Metabolic and Biomolecular Engineering National Research Laboratory | Kim T.Y.,Metabolic and Biomolecular Engineering National Research Laboratory | Lee S.Y.,Metabolic and Biomolecular Engineering National Research Laboratory | Lee S.Y.,Brain Bio
Current Opinion in Microbiology | Year: 2010

Metabolic engineering has enabled us to develop strains suitable for their use as microbial factories of chemicals and materials from renewable sources. It has recently become more powerful with the advanced in synthetic biology, which is allowing us to create novel and fine-controlled metabolic and regulatory circuits maximizing metabolic fluxes to the desired products in the strain being developed. This enables us to engineer host microorganisms to enhance their innate metabolic capabilities or to gain new capabilities in the production of target compounds. Here we review recently constructed synthetic pathways that have been successfully applied for producing non-innate chemicals and also discuss recent approaches developed to increase the efficiency of synthetic pathways for achieving higher productivities of desired bioproducts. © 2010 Elsevier Ltd. All rights reserved.


Kim T.Y.,Metabolic and Biomolecular Engineering National Research Laboratory | Kim T.Y.,KAIST | Kim H.U.,Metabolic and Biomolecular Engineering National Research Laboratory | Kim H.U.,KAIST | And 3 more authors.
Metabolic Engineering | Year: 2010

Development of genome-scale metabolic models and various constraints-based flux analyses have enabled more sophisticated examination of metabolism. Recently reported metabolite essentiality studies are also based on the constraints-based modeling, but approaches metabolism from a metabolite-centric perspective, providing synthetic lethal combination of reactions and clues for the rational discovery of antibacterials. In this study, metabolite essentiality analysis was applied to the genome-scale metabolic models of four microorganisms: Escherichia coli, Helicobacter pylori, Mycobacterium tuberculosis and Staphylococcus aureus. Furthermore, chokepoints, metabolites surrounded by enzymes that uniquely consume and/or produce them, were also calculated based on the network properties of the above organisms. A systematic drug targeting strategy was developed by combining information from these two methods. Final drug target metabolites are presented and examined with knowledge from the literature. © 2009 Elsevier Inc. All rights reserved.


Lee J.,Metabolic and Biomolecular Engineering National Research Laboratory | Lee J.,KAIST | Jang Y.-S.,Metabolic and Biomolecular Engineering National Research Laboratory | Choi S.J.,Metabolic and Biomolecular Engineering National Research Laboratory | And 7 more authors.
Applied and Environmental Microbiology | Year: 2012

Clostridium acetobutylicum naturally produces acetone as well as butanol and ethanol. Since acetone cannot be used as a biofuel, its production needs to be minimized or suppressed by cell or bioreactor engineering. Thus, there have been attempts to disrupt or inactivate the acetone formation pathway. Here we present another approach, namely, converting acetone to isopropanol by metabolic engineering. Since isopropanol can be used as a fuel additive, the mixture of isopropanol, butanol, and ethanol (IBE) produced by engineered C. acetobutylicum can be directly used as a biofuel. IBE production is achieved by the expression of a primary/secondary alcohol dehydrogenase gene from Clostridium beijerinckii NRRL B-593 (i.e., adh B-593) in C. acetobutylicum ATCC 824. To increase the total alcohol titer, a synthetic acetone operon (act operon; adc-ctfA-ctfB) was constructed and expressed to increase the flux toward isopropanol formation. When this engineering strategy was applied to the PJC4BK strain lacking in the buk gene (encoding butyrate kinase), a significantly higher titer and yield of IBE could be achieved. The resulting PJC4BK(pIPA3-Cm2) strain produced 20.4 g/liter of total alcohol. Fermentation could be prolonged by in situ removal of solvents by gas stripping, and 35.6 g/liter of the IBE mixture could be produced in 45 h. © 2012, American Society for Microbiology.


Ravikumar S.,University of Ulsan | Yoo I.-K.,University of Ulsan | Lee S.Y.,Metabolic and Biomolecular Engineering National Research Laboratory | Lee S.Y.,Korea Advanced Institute of Science and Technology | Hong S.H.,University of Ulsan
Bioprocess and Biosystems Engineering | Year: 2011

Zinc ion plays essential roles in biological chemistry. Bacteria acquire Zn 2+ from the environment, and cellular concentration levels are controlled by zinc homeostasis systems. In comparison with other homeostatic systems, the ZraSR two-component system was found to be more efficient in responding to exogenous zinc concentrations. To understand the dynamic response of the bacterium ZraSR two-component system with respect to exogenous zinc concentrations, the genetic circuit of the ZraSR system was integrated with a reporter protein. This study was helpful in the construction of an E. coli system that can display selective metal binding peptides on the surface of the cell in response to exogenous zinc. The engineered bacterial system for monitoring exogenous zinc was successfully employed to detect levels of zinc as low as 0.001 mM, which directly activates the expression of chimeric ompC t -zinc binding peptide gene to remove zinc by adsorbing a maximum of 163.6 μmol of zinc per gram of dry cell weight. These results indicate that the engineered bacterial strain developed in the present study can sense the specific heavy metal and activates a cell surface display system that acts to remove the metal. © 2011 Springer-Verlag.


Hwang K.-S.,Metabolic and Biomolecular Engineering National Research Laboratory | Hwang K.-S.,Korea Advanced Institute of Science and Technology | Kim H.U.,Technical University of Denmark | Kim H.U.,Metabolic and Biomolecular Engineering National Research Laboratory | And 6 more authors.
Biotechnology Advances | Year: 2014

Streptomyces species continue to attract attention as a source of novel medicinal compounds. Despite a long history of studies on these microorganisms, they still have many biochemical mysteries to be elucidated. Investigations of novel secondary metabolites and their biosynthetic gene clusters have been more systematized with high-throughput techniques through inspections of correlations among components of the primary and secondary metabolisms at the genome scale. Moreover, up-to-date information on the genome of Streptomyces species with emphasis on their secondary metabolism has been collected in the form of databases and knowledgebases, providing predictive information and enabling one to explore experimentally unrecognized biological spaces of secondary metabolism. Herein, we review recent trends in the systems biology and biotechnology of Streptomyces species. © 2013 Elsevier Inc.

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