Institute for the BioCentury

Yuseong gu, South Korea

Institute for the BioCentury

Yuseong gu, South Korea

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Jung Y.K.,Institute for the BioCentury | Kim T.Y.,Institute for the BioCentury | Park S.J.,LG Corp | Lee S.Y.,Institute for the BioCentury | Lee S.Y.,Brain Bio
Biotechnology and Bioengineering | Year: 2010

Polylactic acid (PLA) is a promising biomass-derived polymer, but is currently synthesized by a two-step process: fermentative production of lactic acid followed by chemical polymerization. Here we report production of PLA homopolymer and its copolymer, poly(3-hydroxybutyrate-co-lactate), P(3HB-co-LA), by direct fermentation of metabolically engineered Escherichia coli. As shown in an accompanying paper, introduction of the heterologous metabolic pathways involving engineered propionate CoA-transferase and polyhydroxyalkanoate (PHA) synthase for the efficient generation of lactyl-CoA and incorporation of lactyl-CoA into the polymer, respectively, allowed synthesis of PLA and P(3HB-co-LA) in E. coli, but at relatively low efficiency. In this study, the metabolic pathways of E. coli were further engineered by knocking out the ackA, ppc, and adhE genes and by replacing the promoters of the ldhA and acs genes with the trc promoter based on in silico genome-scale metabolic flux analysis in addition to rational approach. Using this engineered strain, PLA homopolymer could be produced up to 11 wt% from glucose. Also, P(3HB-co-LA) copolymers containing 55-86 mol% lactate could be produced up to 56 wt% from glucose and 3HB. P(3HB-co-LA) copolymers containing up to 70 mol% lactate could be produced to 46 wt% from glucose alone by introducing the Cupriavidus necator β-ketothiolase and acetoacetyl-CoA reductase genes. Thus, the strategy of combined metabolic engineering and enzyme engineering allowed efficient bio-based one-step production of PLA and its copolymers. This strategy should be generally useful for developing other engineered organisms capable of producing various unnatural polymers by direct fermentation from renewable resources. © 2009 Wiley Periodicals, Inc.


Malaviya A.,Institute for the BioCentury | Jang Y.-S.,Institute for the BioCentury | Lee S.Y.,Institute for the BioCentury | Lee S.Y.,KAIST
Applied Microbiology and Biotechnology | Year: 2012

Butanol, a four-carbon primary alcohol (C 4H 10O), is an important industrial chemical and has a good potential to be used as a superior biofuel. Bio-based production of butanol from renewable feedstock is a promising and sustainable alternative to substitute petroleum-based fuels. Here, we report the development of a process for butanol production from glycerol, which is abundantly available as a byproduct of biodiesel production. First, a hyper butanol producing strain of Clostridium pasteurianum was isolated by chemical mutagenesis. The best mutant strain, C. pasteurianum MBEL-GLY2, was able to produce 10.8 gl -1 butanol from 80 gl -1 glycerol as compared to 7.6 gl -1 butanol produced by the parent strain. Next, the process parameters were optimized to maximize butanol production from glycerol. Under the optimized batch condition, the butanol concentration, yield, and productivity of 17.8 gl -1, 0.30 gg -1, and 0.43 gl -1 h -1 could be achieved. Finally, continuous fermentation of C. pasteurianum MBEL-GLY2 with cell recycling was carried out using glycerol as a major carbon source at several different dilution rates. The continuous fermentation was run for 710 h without strain degeneration. The acetone-butanol-ethanol productivity and the butanol productivity of 8.3 and 7.8 gl -1 h -1, respectively, could be achieved at the dilution rate of 0.9 h -1. This study reports continuous production of butanol with reduced byproducts formation from glycerol using C. pasteurianum, and thus could help design a bioprocess for the improved production of butanol. © 2011 Springer-Verlag.


Choi B.G.,KAIST | Park H.,Kyung Hee University | Park T.J.,Institute for the BioCentury | Yang M.H.,KAIST | And 7 more authors.
ACS Nano | Year: 2010

We report the preparation of free-standing flexible conductive reduced graphene oxide/Nafion (RGON) hybrid films by a solution chemistry that utilizes self-assembly and directional convective-assembly. The hydrophobic backbone of Nafion provided well-defined integrated structures, on micro- and macroscales, for the construction of hybrid materials through self-assembly, while the hydrophilic sulfonate groups enabled highly stable dispersibility (∼ 0.5 mg/mL) and long-term stability (2 months) for graphene. The geometrically interlocked morphology of RGON produced a high degree of mechanical integrity in the hybrid films, while the interpenetrating network constructed favorable conduction pathways for charge transport. Importantly, the synergistic electrochemical characteristics of RGON were attributed to high conductivity (1176 S/m), facilitated electron transfer (ET), and low interfacial resistance. Consequently, RGON films obtained the excellent figure of merit as electrochemical biosensing platforms for organophosphate (OP) detection, that is, a sensitivity of 10.7 nA/μM, detection limit of 1.37 × 10 -7 M, and response time of <3 s. In addition, the reliability of RGON biosensors was confirmed by a fatigue test of 100 bending cycles. The strategy described here provides insight into the fabrication of graphene and hybrid nanomaterials from a material perspective, as well as the design of biosensor platforms for practical device applications. © 2010 American Chemical Society.


Ahn J.-H.,Institute for the BioCentury | Choi S.-J.,Institute for the BioCentury | Han J.-W.,Institute for the BioCentury | Park T.J.,Institute for the BioCentury | And 4 more authors.
Nano Letters | Year: 2010

A silicon nanowire field effect transistor (FET) straddled by the double-gate was demonstrated for biosensor application. The separated double-gates, G1 (primary) and G2 (secondary), allow independent voltage control to modulate channel potential. Therefore, the detection sensitivity was enhanced by the use of G2. By applying weakly positive bias to G2, the sensing window was significantly broadened compared to the case of employing G1 only, which is nominally used in conventional nanowire FET-based biosensors. The charge effect arising from biomolecules was also analyzed. Double-gate nanowire FET can pave the way for an electrically working biosensor without a labeling process. © 2010 American Chemical Society.


Noh J.-H.,Inha University | Kim S.-H.,Inha University | Lee H.-N.,Inha University | Lee S.Y.,Institute for the BioCentury | Kim E.-S.,Inha University
Applied Microbiology and Biotechnology | Year: 2010

Cross-genome comparative transcriptome analyses were previously conducted using the sequenced Streptomyces coelicolor genome microarrays to understand the genetic nature of doxorubicin (DXR) and daunorubicin (DNR) overproducing industrial mutant (OIM) of Streptomyces peucetius. In this previous work, a whiB-like putative transcription factor (wblAsco) was identified as a global antibiotic down-regulator in S. coelicolor (Kang et al., J Bacteriol 189:4315-4319, 2007). In this study, a total genomic DNA library of a DXR/DNR-overproducing S. peucetius OIM was constructed and screened using wblAsco as a probe, resulting in the isolation of a wblA ortholog (wblA spe) that had 95% amino acid identity to wblAsco. Gene disruption of wblAspe from the S. peucetius OIM resulted in an approximately 70% increase in DXR/DNR productivity, implying that the DXR/DNR production in the S. peucetius OIM could be further improved via comparative transcriptomics-guided target gene manipulation. Furthermore, several putative wblAspe-dependent genes were also identified using S. coelicolor interspecies DNA microarray analysis between the S. peucetius OIM and wblA spe-disrupted S. peucetius OIM. Among the genes whose expressions were significantly stimulated in the absence of wblAspe, the overexpression of a conserved hypothetical protein (SCO4967) further stimulated the total production of DXR/ DNR/akavinone by 1.3-fold in the wblA spe-disrupted S. peucetius OIM, implying that the sequential genetic manipulation of target genes identified from interspecies comparative microarray analysis could provide an efficient and rational strategy for Streptomyces strain improvement. © 2009 Springer-Verlag.


Kim Y.-K.,Institute for the BioCentury | Na H.-K.,Institute for the BioCentury | Kwack S.-J.,Institute for the BioCentury | Ryoo S.-R.,Institute for the BioCentury | And 4 more authors.
ACS Nano | Year: 2011

Matrix-assisted laser desorption/ionization mass spectrometry has been considered an important tool for various biochemical analyses and proteomics research. Although addition of conventional matrix efficiently supports laser desorption/ionization of analytes with minimal fragmentation, it often results in high background interference and misinterpretation of the spatial distribution of biomolecules especially in low-mass regions. Here, we show design, systematic characterization, and application of graphene oxide/multiwalled carbon nanotube-based films fabricated on solid substrates as a new matrix-free laser desorption/ionization platform. We demonstrate that the graphene oxide/multiwalled carbon nanotube double layer provides many advantages as a laser desorption/ionization substrate, such as efficient desorption/ionization of analytes with minimum fragmentation, high salt tolerance, no sweet-spots for mass signal, excellent durability against mechanical and photoagitation and prolonged exposure to ambient conditions, and applicability to tissue imaging mass spectrometry. This platform will be widely used as an important tool for mass spectrometry-based biochemical analyses because of its outstanding performance, long-term stability, and cost effectiveness. © 2011 American Chemical Society.


Jung J.H.,Institute for the BioCentury | Park T.J.,Institute for the BioCentury | Lee S.Y.,Institute for the BioCentury | Seo T.S.,Institute for the BioCentury
Angewandte Chemie - International Edition | Year: 2012

All under control: A microfluidic droplet generator uniformly encapsulates an equivalent number of engineered E. coli cells and the same Fe and Mn metal ion concentrations in identically sized droplets. The synthesized biogenic FeMn paramagnetic nanoparticles inside the cells are eco-friendly and cost-effective. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Cho C.,Institute for the BioCentury | Lee S.Y.,Institute for the BioCentury
Biotechnology and Bioengineering | Year: 2016

Clostridium is considered a promising microbial host for the production of valuable industrial chemicals. However, Clostridium is notorious for the difficulty of genetic manipulations, and consequently metabolic engineering. Thus, much effort has been exerted to develop novel tools for genetic and metabolic engineering of Clostridium strains. Here, we report the development of a synthetic small regulatory RNA (sRNA)-based system for controlled gene expression in Clostridium acetobutylicum, consisting of a target recognition site, MicC sRNA scaffold, and an RNA chaperone Hfq. To examine the functional operation of sRNA system in C. acetobutylicum, expression control was first examined with the Evoglow fluorescent protein as a model protein. Initially, a C. acetobutylicum protein annotated as Hfq was combined with the synthetic sRNA based on the Escherichia coli MicC scaffold to knockdown Evoglow expression. However, C. acetobutylicum Hfq did not bind to E. coli MicC, while MicC scaffold-based synthetic sRNA itself was able to knockdown the expression of Evoglow. When E. coli hfq gene was introduced, the knockdown efficiency assessed by measuring fluorescence intensity, could be much enhanced. Then, this E. coli MicC scaffold-Hfq system was used to knock down adhE1 gene expression in C. acetobutylicum. Knocking down the adhE1 gene expression using the synthetic sRNA led to a 40% decrease in butanol production (2.5g/L), compared to that (4.5g/L) produced by the wild-type strain harboring an empty vector. The sRNA system was further extended to knock down the pta gene expression in the buk mutant C. acetobutylicum strain PJC4BK for enhanced butanol production. The PJC4BK (pPta-HfqEco) strain, which has the pta gene expression knocked down, was able to produce 16.9g/L of butanol, which is higher than that (14.9g/L) produced by the PJC4BK strain, mainly due to reduced acetic acid production. Fed-batch culture of PJC4BK (pPta-HfqEco) strain coupled with in situ gas stripping produced 105.5g of total solvents (70.7g butanol, 20.5g acetone, and 14.3g ethanol), demonstrating that the sRNA-based engineered C. acetobutylicum strain can be cultured without instability. The synthetic sRNA system reported in this study will be useful for more efficient development of engineered C. acetobutylicum strains capable of producing valuable chemicals and fuels. © 2016 Wiley Periodicals, Inc.


Yim H.,Genomatica | Haselbeck R.,Genomatica | Niu W.,Genomatica | Pujol-Baxley C.,Genomatica | And 14 more authors.
Nature Chemical Biology | Year: 2011

1,4-Butanediol (BDO) is an important commodity chemical used to manufacture over 2.5 million tons annually of valuable polymers, and it is currently produced exclusively through feedstocks derived from oil and natural gas. Herein we report what are to our knowledge the first direct biocatalytic routes to BDO from renewable carbohydrate feedstocks, leading to a strain of Escherichia coli capable of producing 18 g l 1 of this highly reduced, non-natural chemical. A pathway-identification algorithm elucidated multiple pathways for the biosynthesis of BDO from common metabolic intermediates. Guided by a genome-scale metabolic model, we engineered the E. coli host to enhance anaerobic operation of the oxidative tricarboxylic acid cycle, thereby generating reducing power to drive the BDO pathway. The organism produced BDO from glucose, xylose, sucrose and biomass-derived mixed sugar streams. This work demonstrates a systems-based metabolic engineering approach to strain design and development that can enable new bioprocesses for commodity chemicals that are not naturally produced by living cells. © 2011 Nature America, Inc. All rights reserved.


Kim Y.,Korea Advanced Institute of Science and Technology | Jeong H.,Korea Advanced Institute of Science and Technology | Jeong H.,Institute for the BioCentury
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2011

Community structure exists in many real-world networks and has been reported being related to several functional properties of the networks. The conventional approach was partitioning nodes into communities, while some recent studies start partitioning links instead of nodes to find overlapping communities of nodes efficiently. We extended the map equation method, which was originally developed for node communities, to find link communities in networks. This method is tested on various kinds of networks and compared with the metadata of the networks, and the results show that our method can identify the overlapping role of nodes effectively. The advantage of this method is that the node community scheme and link community scheme can be compared quantitatively by measuring the unknown information left in the networks besides the community structure. It can be used to decide quantitatively whether or not the link community scheme should be used instead of the node community scheme. Furthermore, this method can be easily extended to the directed and weighted networks since it is based on the random walk. © 2011 American Physical Society.

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