Research

1.  Metabolic Engineering (systems metabolic engineering) 

We have established the biotechnology field named 'systems metabolic engineering' for industrial biotechnology. Systems metabolic engineering is an evolved version of traditional metabolic engineering wherein other systematic and high-throughput fields are also integrated as a coherent discipline, including "systems biology (e.g., omics analysis and genome-scale computational simulation), synthetic biology (e.g., various molecular approaches, tools and pathway modules allowing fine control and regulation of gene expression levels and precise genome engineering) and evolutionary engineering (e.g., laboratory evolution of cells for enhanced product tolerance), while continuing to consider upstream (strain development) to midstream (fermentation) to downstream (separation and purification) processes as a whole" (Lee and Kim, Nature Biotechnology, 2015).

Concept of the systems metabolic engineering framework

(Lee and Kim, Nature Biotechnology, 2015).

367. "Systems metabolic engineering of microorganisms for natural and non-natural chemicals" (2012)

336. "Systems metabolic engineering for chemicals and materials" (2011)

223. "Application of systems biology for bioprocess development" (2008)


We apply the systems metabolic engineering framework for microbial production of a wide range of bioproducts that are important in industrial biotechnology. Representative microbial bioproducts produced in MBEL are as follows:

2.  Synthetic Biology

Efficient molecular tools are prerequisite to designing and constructing high-performance microbial strains. By incorporating the synthetic biology principle and state-of-the-art genome engineering strategies, we develop powerful molecular tools to manipulate bacterial genomes and fine-tune metabolic fluxes.

Development of CRISPR/Cas9-based genome editing system for Corynebacterium glutamicum

(Cho et al., Metabolic Engineering, 2017). 

Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli

(Yoo et al., Nature Protocols, 2013) 

Development and application of synthetic sRNA-based strategy for large-scale target

identification and fine-tuning of gene expression for the enhanced production.

(Na et al., Nature Biotechnology, 2013). 

Development of a rapid one-step inactivation of single or multiple genes in Escherichia coli.

(Song et al., Biotechnology Journal, 2013). 

457. "CRISPR-Cas9 based engineering of actinomycetal genomes" (2015)

434. "Genome engineering and gene expression control for bacterial strain development" (2015)

3.  Systems Biology, Bioinformatics and AI

Systems biology (or in silico biology) has been another important research domain of MBEL, and has been actively deployed in implementing systems metabolic engineering. For this, we develop computational models and methods, and apply them to various biotechnology problems. To this end, we develop genome-scale metabolic models (GEMs) of a series of bacteria that are important in industrial biotechnology. While we take genome-scale metabolic modeling as a general starting point of systems biology studies, we also actively adopt various complementary computational technologies covering bioinformatics, cheminformatics and machine learning (e.g., deep learning), depending on the problem definition. 

Development of a genome-scale metabolic model of a succinic acid overproducing bacterium

Mannheimia succiniciproducens 

(Kim et al., Biotechnology and Bioengineering, 2007). 

Development of a genome-scale metabolic model of an opportunistic human pathogen

 Vibrio vulnificus for its use in effective antibiotic targeting and discovery 

(Kim et al., Molecular Systems Biology, 2011). 

Schematic illustration of accurate prediction of intracellular flux distribution using grouping reaction constraints 

(Park et al., PNAS, 2010). 

293. "in silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics, and anaerobic survival" (2010)

292. "Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production" (2010)

287. "in silico identification of gene amplification targets for improving lycopene production" (2010)

278. "Data integration and analysis of biological networks" (2010)

269. "Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE" (2010)

199. "Metabolite essentiality elucidates robustness of Escherichia coli metabolism" (2007)

197. "EcoProDB: the Escherichia coli protein database" (2007)

176. "WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks" (2006)

175. "The Escherichia coli Proteome: Past, Present, and Future Prospects" (2006)

164. "Enhanced Proteome Profiling by Inhibiting Proteolysis with Small Heat Shock Proteins" (2005)

157. "MFAML: a standard data structure for representing and exchanging metabolic flux models" (2005)

147. "The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens" (2004)

140. "BioSilico: an integrated metabolic database system" (2004)

137. "Roles and applications of small heat shock proteins in the production of recombinant proteins in Escherichia coli" (2004)

135. "Phylogenetic analysis based on genome-scale metabolic pathway reaction content" (2004)

114. "MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis" (2003)

107. "Combined transcriptome and proteome analysis of Escherichia coli during high cell density culture" (2003)

4.  Industrial biotechnology: Chemicals and materials

We have developed microorganisms that produce various biopolymers, representatively polyhydroxyalkanoates (PHAs) and spider-silk proteins. PHAs are bacterial polyesters which are accumulated as carbon/energy storage materials in several microorganisms under specific cultivation conditions. Thanks to the biodegradability and mechanical properties similar to the commodity plastics, PHAs have drawn attention for commercial applications. To date, we have published more than 90 studies on PHAs. Our representative achievements include production of non-natural PHAs including poly(lactate)[PLA] (Jung et al., Biotechnology and Bioengineering, 2010), poly(lactate-co-glycolate)[PLGA] (Choi et al., Nature Biotechnology, 2016) and aromatic PHAs (Yang et al., Nature Communications, 2018). Our microbial system is able to produce various useful plastics in a sustainable and environment-friendly manner.

Development of recombinant E. coli strains producing PLA (Jung et al., Biotechnology and Bioengineering, 2010),

PLGA (Choi et al., Nature Biotechnology, 2016) and PHAs containing aromatic monomers

(Yang et al., Nature Communications, 2018).


 We are also interested in producing different types of biopolymers, a representative example being spider silk protein that has important implications in both materials and biomedical industries. We previously produced the spider silk protein for the first time in Escherichia coli, which showed remarkable mechanical properties comparable to those of Kevlar, the strongest man-made fiber existing.

Recombinant expression of spider dragline silk proteins in Escherichia coli

(Xia et al., PNAS, 2010).


 We also use bacteria to produce various forms of biofuels beyond bioethanol in order to meet demands of various sectors of the industry and society. To date, we have constructed microbial systems that produce butanol, diesel, alkane and alkene.

Development of an Escherichia coli strain producing short-chain alkane that can be used as gasoline

(Choi and Lee, Nature, 2013).

Development of an Escherichia coli strain producing short-chain alkane that can be used as gasoline

(Choi and Lee, Nature, 2013).

We have developed microbial strains that produce a variety of industrial chemicals by applying systems metabolic engineering technology. Together with the strain development, fermentation process optimization is performed to produce target chemicals to the maximally possible extent. The industrial chemicals that we successfully produced include, but not limited to, succinic acid, fumaric acid, malic acid, terephthalic acid, 1,3-propanediol, 1,3-diaminopropane, 4-hydroxybutric acid, 3-hydroxypropionic acid, malonic acid, 5-aminovaleric acid, ethylene glycol, butyric acid, putrescine, and cadaverine.

Microbial production of 3-hydroxypropionic acid and malonic acid

(Song et al., ACS Synthetic Biology, 2016).

497. "Structure and function of the N-terminal domain of Ralstonia eutropha polyhydroxyalkanoate synthase, and the proposed structure and mechanisms of the whole enzyme" (2017)

496. "Crystal structure of Ralstonia eutropha polyhydroxyalkanoate synthase C-terminal domain and reaction mechanisms" (2017)

493. "Biosynthesis of poly(2-hydroxyisovalerate-co-lactate) by metabolically engineered Escherichia coli" (2016)

466. "Recent advances in biobutanol production" (2015)

459. "Redox-switch regulatory mechanism of thiolase from Clostridium acetobutylicum" (2015)

429. "Metabolic engineering of microorganisms for the production of higher alcohols" (2014)

428. "Metabolic engineering of Corynebacterium glutamicum for L-arginine production" (2014)

399. "Metabolic engineering of Escherichia coli for the production of fumaric acid" (2013)

385. "Rational design of Escherichia coli for L-isoleucine production" (2012)

370. "Bio-based production of C2-C6 platform chemicals" (2012)

362. "One-step fermentative production of polylactic acid (PLA)" (2012)

361. "Microbial metabolic engineering for the production of polyesters" (2012)

354. "Biosynthesis of lactate containing polyesters by metabolically engineered bacteria" (2012)

353. "Butanol production from renewable biomass: rediscovery of metabolic pathways and metabolic engineering" (2012)

338. "Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol" (2011)

258. "Metabolic engineering of Escherichia coli for the production of putrescine, a four carbon diamine" (2009)

255. "Metabolic engineering of Clostridium acetobutylicum M5 for highly selective butanol production" (2009)

230. "Towards systems metabolic engineering of microorganisms for amino acid production" (2008)

226. "Proteome-based identification of fusion partner for high-level extracellular production of recombinant proteins in Escherichia coli" (2008)

202. "Systems metabolic engineering of Escherichia coli for L-threonine production" (2007)

194. "Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation" (2007)

187. "Deciphering bioplastic production" (2006)

171. "Genome-based metabolic engineering of Mannheimia succiniciproducens for succinic acid production" (2006)

147. "The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens" (2004)

32. "E. coli moves into the plastic age" (1997)

5.  Natural products

Microbial production of natural compounds is also of our interest as they provide very specialized useful functions, such as antioxidant, antibiotic and anticancer. It is usually difficult to chemically synthesize natural products, and therefore microbial biosynthesis can be a great solution for the enhanced production.

General scheme of developing microbial cell factories for natural compounds production

(Park et al., Advanced Biosystems, 2018).

Schematic representation of optimized indirubin biosynthetic pathway in Escherichia coli

(Du et al., Journal of Biotechnology, 2018).

Metabolic simulation-driven optimization of lycopene biosynthetic pathway in Escherichia coli

and a picture taken during fed-batch fermentation of lycopene-producing E. coli

(Choi et al., Applied and Environmental Microbiology, 2010).

502. "Polyketide bio-derivatization using the promiscuous acyltransferase KirCII" (2017)

433. "Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes" (2015)

6.  Systems medicine, precision medicine and microbiome research

 We also use systems biology, bioinformatics and AI approaches to solve various medical problems, including antibiotics and anticancer discovery. For this purpose, we recently developed a generic human cell system that can be used in systems medicine and precision medicine problems. Our research efforts in this field are continuing to grow.

Development of a genome-scale metabolic model of a generic human cell with information

on alternative spicing (Ryu et al., PNAS, 2017).

Use of human genome-scale metabolic models to elucidate reprogrammed metabolism of

liver cancer stem cells (LCSCs) compared with non-LCSCs, which can be highlighted

by more active glycolysis and glutaminolysis (red lines) and relatively inhibited fatty acid oxidation (blue lines).

Dotted line indicates indirect regulations through signaling cascade. (Hur et al., Scientific Reports, 2017)

Use of chemical structural analysis for the characterization of compounds found in traditional oriental medicine

(Kim et al., Nature Biotechnology, 2015).

512. "Holographic deep learning for rapid optical screening of anthrax spores" (2017)

507. "Dissemination of antibiotic resistance genes from antibiotic producers to pathogens" (2017)

359. "Metabolic network modeling and simulation for drug targeting and discovery" (2012)

7.  Nanobiotechnology

We also explore nanobiotechnology, developing platform technologies for the detection of pathogens and/or other (often toxic) chemicals of interest, and microbially producing various nanomaterials with unique physical properties. Our representative achievement is on biosynthesizing diverse nanomaterials, and the extended, exciting studies are currently ongoing.

In vitro biosynthesis of metal nanoparticles in microdroplets

(Lee et al., ACS Nano, 2012)

In vitro synthesis of diverse metal nanoparticles by recombinant Escherichia coli

(Park et al., Angewandte Chemie International Edition, 2010)

365. "Homogeneous biogenic paramagnetic nanoparticle synthesis based on a microfluidic droplet generator" (2012)

347. "Combining nanowire SERRS sensor and target recycling reaction for ultrasensitive and multiplex identification of pathogenic fungi" (2011)

282. "Patterned multiplex pathogen DNA detection by Au particle-on-wire SERS sensor" (2010)

280. "DNA microarray for the identification of pathogens causing bloodstream infections" (2010)

191. "Development of DNA chip for the diagnosis of most common corneal dystrophies caused by mutations in the bigh3 gene" (2007)

131. "Microarrays of peptides elevated on the protein layer for efficient protein kinase assay" (2004)