The Systems Bioengineering Laboratory was founded in 2004 by Professor Min-kyu Oh within the Department of Chemical and Biological Engineering at Korea University. The laboratory is located in the New Engineering Building and focuses on metabolic engineering, synthetic biology, and systems bioengineering.

고려대학교 화학생물공학과 오민규 교수가 2004년 시스템 생물공학 연구실을 설립했다. 주요 연구 시설은 신공학관에 위치하며, 대사 공학, 합성 생물학, 시스템 생물공학을 주요 연구 분야로 한다.

Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects

Global expression profiling of acetate-grown Escherichia coli∗

Engineered isoprenoid pathway enhances astaxanthin production in Escherichia coli

Production of 2, 3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering

Gene Expression Profiling by DNA Microarrays and Metabolic Fluxes in Escherichiacoli

Co-expression pattern from DNA microarray experiments as a tool for operon prediction

Directed Evolution of Metabolically Engineered Escherichia coli for Carotenoid Production

Characterization of poly-3-hydroxybutyrate (PHB) produced from Ralstonia eutropha using an alkali-pretreated biomass feedstock

In Situ Biphasic Extractive Fermentation for Hexanoic Acid Production from Sucrose by Megasphaera elsdenii NCIMB 702410

A sensitive method to detect Escherichia coli based on immunomagnetic separation and real-time PCR amplification of aptamers

Deletion of lactate dehydrogenase in Enterobacter aerogenes to enhance 2, 3-butanediol production

DNA microarray detection of metabolic responses to protein overproduction in Escherichia coli

Butyrate production in engineered Escherichia coli with synthetic scaffolds

A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae

Applications and advances in bioelectronic noses for odour sensing

Biosynthesis of 2-phenylethanol from glucose with genetically engineered Kluyveromyces marxianus

Microbial production of 2, 3 butanediol from seaweed hydrolysate using metabolically engineered<i> Escherichia coli

Photosensitizer and vancomycin-conjugated novel multifunctional magnetic particles as photoinactivation agents for selective killing of pathogenic bacteria

Nearly carbon-free printable CIGS thin films for solar cell applications

Production of 1, 2-Propanediol from Glycerol in Saccharomyces cerevisiae

Microbial production of 2, 3 butanediol from seaweed hydrolysate using metabolically engineered< i> Escherichia coli</i>

Moo-Young Jung

Kyung Woo Kim

Dae Kyun Im

Sang-Woo Lee

Hwi-Min Jung

Dong June Ahn

Byoung-In Sang

Gyoo Yeol Jung

Jungbae Kim

Byoung Chan Kim

Sang Heum Shin

George Tseng

Chiam Yu Ng

Prof. S.P. Govindwar

Sang Yup Lee

Katy C. Kao

Sang Woo Seo

Beom Soo Kim

Robert J. Mitchell

Kyoung-Soon Jang

Min-Kyu Oh

We consider the problem of comparing the gene expression levels of cells grown under two different conditions using cDNA microarray data. We use a quality index, computed from duplicate spots on the same slide, to filter out outlying spots, poor quality genes and problematical slides. We also perform calibration experiments to show that normalization between fluorescent labels is needed and that the normalization is slide dependent and non-linear. A rank invariant method is suggested to select non-differentially expressed genes and to construct normalization curves in comparative experiments. After normalization the residuals from the calibration data are used to provide prior information on variance components in the analysis of comparative experiments. Based on a hierarchical model that incorporates several levels of variations, a method for assessing the significance of gene effects in comparative …

This study characterized the transcript profile of Escherichia coli in acetate cultures using DNA microarray on glass slides. Glucose-grown cultures were used as a reference. At the 95% confidence level, 354 genes were up-regulated in acetate, while 370 genes were down-regulated compared with the glucose-grown culture. Generally, more metabolic genes were up-regulated in acetate than other gene groups, while genes involved in cell replication, transcription, and translation machinery tended to be down-regulated. It appears that E. coli commits more resources to metabolism at the expense of growth when cultured in the poor carbon source. The expression profile confirms many known features in acetate metabolism such as the induction of the glyoxylate pathway, tricarboxylic acid cycle, and gluconeogenic genes. It also provided many previously unknown features, including induction of malic enzymes …

The isoprenoid pathway is a versatile biosynthetic network leading to over 23,000 compounds. Similar to other biosynthetic pathways, the production of isoprenoids in microorganisms is controlled by the supply of precursors, among other factors. To engineer a host that has the capability to supply geranylgeranyl diphosphate (GGPP), a common precursor of isoprenoids, we cloned and overexpressed isopentenyl diphosphate (IPP) isomerase (encoded by idi ) from Escherichia coli and GGPP synthase (encoded by gps ) from the archaebacterium Archaeoglobus fulgidus. The latter was shown to be a multifunctional enzyme converting dimethylallyl diphosphate (DMAPP) to GGPP. These two genes and the gene cluster ( crtBIYZW ) of the marine bacterium Agrobacterium aurantiacum were introduced into E. coli to produce astaxanthin, an orange pigment and antioxidant. This metabolically engineered strain produces …

Background 2,3-Butanediol is a chemical compound of increasing interest due to its wide applications. It can be synthesized via mixed acid fermentation of pathogenic bacteria such as Enterobacter aerogenes and Klebsiella oxytoca. The non-pathogenic Saccharomyces cerevisiae possesses three different 2,3-butanediol biosynthetic pathways, but produces minute amount of 2,3-butanediol. Hence, we attempted to engineer S. cerevisiae strain to enhance 2,3-butanediol production. Results We first identified gene deletion strategy by performing in silico genome-scale metabolic analysis. Based on the best in silico strategy, in which disruption of alcohol dehydrogenase (ADH) pathway is required, we then constructed gene deletion mutant strains and performed batch cultivation of the strains. Deletion of three ADH genes, ADH1, ADH3 and ADH5, increased 2,3-butanediol production by 55-fold under microaerobic …

DNA microarray technology was applied to detect differential transcription profiles of a subset of the Escherichia coli genome. A total of 111 E. coli genes, including those in central metabolism, key biosyntheses, and some regulatory functions, were cloned, amplified, and used as probes for detecting the level of transcripts. An E. coli strain was grown in glucose, acetate, and glycerol media, and the transcript levels of the selected genes were detected. Despite extensive studies on E. coli physiology, many new features were found in the regulation of these genes. For example, several genes were unexpectedly up‐regulated, such as pps , ilvG , aroF , secA , and dsbA in acetate and asnA and asnB in glycerol, or down‐regulated, such as ackA , pta , and adhE in acetate. These genes were regulated with no apparent reasons by unknown mechanisms. Meanwhile, many genes were regulated for apparent purposes but by …

The prediction of operons, the smallest unit of transcription in prokaryotes, is the first step towards reconstruction of a regulatory network at the whole genome level. Sequence information, in particular the distance between open reading frames, has been used to predict if adjacent Escherichia coli genes are in an operon. While appreciably successful, these predictions need to be validated and refined experimentally. As a growing number of gene expression array experiments on E.coli became available, we investigated to what extent they could be used to improve and validate these predictions. To this end, we examined a large collection of published microarry data. The correlation between expression ratios of adjacent genes was used in a Bayesian classification scheme to predict whether the genes are in an operon or not. We found that for the genes whose expression …

We have previously introduced a reconstructed isoprenoid pathway into Escherichia coli that exhibits amplified biosynthetic flux to geranylgeranyl diphosphate (GGPP), a common isoprenoid precursor. It was shown that GGPP synthase is an important rate‐controlling enzyme in this reconstructed isoprenoid pathway. In this investigation, we applied directed evolution to GGPP synthase from Archaeoglobus fulgidus to enable the enhanced production of carotenoids in metabolically engineered E. coli . Eight mutants were isolated, and the best one increased lycopene production by 100%. Among the mutants that were isolated, mutation points were clustered in four “hot regions”. The “hottest” region is located in the sequence upstream of the coding region, which presumably improves the expression level of the enzyme. The other three are within the coding sequence and are believed to improve the enzyme‐specific …

Alkaline pretreatment using NaOH, KOH, or NaOCl has been applied to various types of waste biomass to enhance enzymatic digestibility. Pretreatment (2% NaOH, 121 °C, 30 min) of rice paddy straw (PS) resulted in a maximum yield of 703 mg of reducing sugar per gram of PS with 84.19% hydrolysis yield after a two-step enzymatic hydrolysis process. Ralstonia eutropha ATCC 17699 was tested for its ability to synthesize poly-3-hydroxybutyrate (PHB) using PS hydrolysates as its sole carbon source. It is noteworthy that dry cell weight, polyhydroxyalkanoate (PHA) accumulation and PHB yield with the use of laboratory-grade sugars were similar to those achieved with PS-derived sugars. Under optimized conditions, we observed maximal PHA accumulation (75.45%) and PHB production (11.42 g/L) within 48 h of fermentation. After PHB recovery, the physicochemical properties of PHB were determined by various …

Hexanoic acid production by a bacterium using sucrose as an economic carbon source was studied under conditions in which hexanoic acid was continuously extracted by liquid–liquid extraction. Megasphaera elsdenii NCIMB 702410, selected from five M . elsdenii strains, produced 4.69 g l −1 hexanoic acid in a basal medium containing sucrose. Production increased to 8.19 g l −1 when the medium was supplemented by 5 g l −1 sodium butyrate. A biphasic liquid–liquid extraction system with 10 % ( v / v ) alamine 336 in oleyl alcohol as a solvent was evaluated in a continuous stirred-tank reactor held at pH 6. Over 90 % ( w / w ) of the hexanoic acid in a 0.5 M aqueous solution was transferred to the extraction solvent within 10 h. Cell growth was not significantly inhibited by direct contact of the fermentation broth with the extraction solvent. The system produced 28.42 g l −1 of hexanoic acid from 54.85 g l −1 of sucrose …

Aptamers, single-stranded nucleic acids, provide a unique opportunity as amplifiable molecules using polymerase chain reaction (PCR) as well as recognition molecules like antibodies. We report a highly sensitive detection of Escherichia coli by taking advantage of the aptamer amplification as well as the specific binding of aptamers onto E. coli. This unique approach consists of three steps. First, the target E. coli was captured by antibody-conjugated magnetic beads. Second, the RNA aptamers were bound onto the surface of captured E. coli in a sandwich way. Finally, the heat-released aptamers were amplified by using real-time reverse-transcriptase-PCR (RT-PCR). The aptamer amplification in this approach has enabled a sensitive detection of microorganisms, such as the detection of 10 E. coli in 1ml sample. When compared to the amplification of nucleic acids extracted from the target microorganisms, this …

2,3-Butanediol is an important bio-based chemical product, because it can be converted into several C4 industrial chemicals. In this study, a lactate dehydrogenase-deleted mutant was constructed to improve 2,3-butanediol productivity in Enterobacter aerogenes . To delete the gene encoding lactate dehydrogenase, λ Red recombination method was successfully adapted for E. aerogenes . The resulting strain produced a very small amount of lactate and 16.7% more 2,3-butanediol than that of the wild-type strain in batch fermentation. The mutant and its parental strain were then cultured with six different carbon sources, and the mutant showed higher carbon source consumption and microbial growth rates in all media. The 2,3-butanediol titer reached 69.5 g/l in 54 h during fed-batch fermentation with the mutant, which was 27.4% higher than that with the parental strain. With further optimization of the medium and …

It has been commonly observed that gratuitous overexpression of proteins in Escherichia coli causes growth retardation. However, the molecular events involved in the metabolic response to the over-expression of proteins are still unclear. Here we used DNA microarray technology to characterize the changes in transcriptional patterns of selected host genes during protein overexpression. A nontoxic, soluble protein, LuxA (coded by luxA), which is the α-subunit of the luciferase heterodimer, was overexpressed for this purpose. A total of 132 E. coli genes, including those in the central metabolism, key biosynthetic pathways, and selected regulatory functions, were used as probes for detecting the level of mRNA transcripts in E. coli strains JM109, MC4100, and VJS676A during protein overexpression. Upon induction, these strains shared several common responses, such as the upregulation of glk and the heat shock …

Butyrate pathway was constructed in recombinant Escherichia coli using the genes from Clostridium acetobutylicum and Treponema denticola . However, the pathway constructed from exogenous enzymes did not efficiently convert carbon flux to butyrate. Three steps of the productivity enhancement were attempted in this study. First, pathway engineering to delete metabolic pathways to by‐products successfully improved the butyrate production. Second, synthetic scaffold protein that spatially co‐localizes enzymes was introduced to improve the efficiency of the heterologous pathway enzymes, resulting in threefold improvement in butyrate production. Finally, further optimizations of inducer concentrations and pH adjustment were tried. The final titer of butyrate was 4.3 and 7.2 g/L under batch and fed‐batch cultivation, respectively. This study demonstrated the importance of synthetic scaffold protein as a useful tool …

Artificial devices such as the synthetic riboswitch have shown potential to introduce unnatural phenotypic perturbation because its synthetic traits are distinct from that of innate metabolism. In this study, a riboswitch, a small regulatory element found in RNAs, was employed to reprogram microorganisms to produce valuable metabolites. A self-cleaving ribozyme glmS , found in gram-positive bacteria, cleaves its own transcript in response to the intracellular glucosamine 6-phosphate (GlcN6P) concentration. The glmS ribozyme was integrated into the 3′-untranslated region of FCY1 , which encodes cytosine deaminase in Saccharomyces cerevisiae to construct a suicide riboswitch for evolutionary engineering. Growth of the strain harboring the suicide riboswitch was hampered by the addition of fluorocytosine, and was recovered as metabolite level increased. By using this riboswitch, we isolated a N-acetyl …

A bioelectronic nose, an intelligent chemical sensor array system coupled with bio-receptors to identify gases and vapours, resembles mammalian olfaction by which many vertebrates can sniff out volatile organic compounds (VOCs) sensitively and specifically even at very low concentrations. Olfaction is undertaken by the olfactory system, which detects odorants that are inhaled through the nose where they come into contact with the olfactory epithelium containing olfactory receptors (ORs). Because of its ability to mimic biological olfaction, a bio-inspired electronic nose has been used to detect a variety of important compounds in complex environments. Recently, biosensor systems have been introduced that combine nanoelectronic technology and olfactory receptors themselves as a source of capturing elements for biosensing. In this article, we will present the latest advances in bioelectronic nose technology mimicking the olfactory system, including biological recognition elements, emerging detection systems, production and immobilization of sensing elements on sensor surface, and applications of bioelectronic noses. Furthermore, current research trends and future challenges in this field will be discussed.

2-Phenylethanol (2-PE) is an aromatic alcohol with a rose scent, which is used in the cosmetics, fragrance and food industries. 2-PE is produced in a few yeast strains by Ehrlich pathway. In this study, Kluyveromyces marxianus was genetically engineered for overproduction of 2-PE from glucose. About 1.0 g/L of 2-PE was produced by overexpressing phenylpyruvate decarboxylase ( ARO10 ) and alcohol dehydrogenase ( ADH2 ) genes of Saccharomyces cerevisiae . A similar level of 2-PE was also produced from evolved K. marxianus , which was resistant to the phenylalanine analog, p -fluorophenylalanine. aroG fbr from Klebsiella pneumoniae encoding a feedback resistant mutant of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DHAP) synthase was overexpressed in the evolved K. marxianus . Finally, 1.3 g/L of 2-PE was produced from 20 g/L glucose without addition of phenylalanine in the medium.

A variety of biofuel and biorefinery products have been produced from engineered Escherichia coli till date. Most of these products had been derived from simple sugars in its pure form, rather than deriving it from alternative, renewable and carbon neutral sources, such as marine alga biomass. Engineering E. coli to use algal hydrolysate can make these an attractive carbon source for the industrial production of value added fuels and chemicals. This work reports the engineering of E. coli by a combination of gene deletion and synthetic pathway incorporation, for the efficient utilization of algal hydrolysate to produce BA (2,3 butanediol+acetoin) under microaerobic condition. Engineered strain produced ∼19g/L of total BA from algal hydrolysate in defined M9 salt media at a yield of 0.43g/g.

Novel multifunctional magnetic particles (MMPs) conjugated with photosensitizer and vancomycin were fabricated by surface modification of Fe3O4 particles. The capacities to target, capture and inactivate pathogenic bacteria and good biocompatibility suggest that the MMPs have great potentials as photodynamic inactivation agents for serious bacterial contamination.

In order to fabricate low cost and printable CuIn x Ga 1−x Se y S 2−y (CIGS) thin film solar cells, a precursor solution based method was developed. Particularly, in this method, nearly carbon-free CIGS film was obtained by applying a three-step heat treatment process: the first for the elimination of carbon residue by air annealing, the second for the formation of CIGS alloy by sulfurization, and the third for grain growth and densification in the CIGS film by selenization. The film also revealed very large grains with a low degree of porosity, similar to those produced by the vacuum based method. A solar cell device with this film showed current–voltage characteristics of J sc =21.02mA/cm 2 , V oc =451mV, FF=47.3%, and η=4.48% at standard conditions.

Glycerol has become an attractive carbon source in the biotechnology industry owing to its low price and reduced state. However, glycerol is rarely used as a carbon source in Saccharomyces cerevisiae because of its low utilization rate. In this study, we used glycerol as a main carbon source in S. cerevisiae to produce 1, 2-propanediol. Metabolically engineered S. cerevisiae strains with overexpression of glycerol dissimilation pathway genes, including glycerol kinase (GUT1), glycerol 3-phosphate dehydrogenase (GUT2), glycerol dehydrogenase (gdh), and a glycerol transporter gene (GUP1), showed increased glycerol utilization and growth rate. More significant improvement of glycerol utilization and growth rate was accomplished by introducing 1, 2-propanediol pathway genes, mgs (methylglyoxal synthase) and gldA (glycerol dehydrogenase) from Escherichia coli. By engineering both glycerol dissimilation and 1, 2-propanediol pathways, the glycerol utilization and growth rate were improved 141% and 77%, respectively, and a 2.19 g 1, 2-propanediol/l titer was achieved in 1%(v/v) glycerolcontaining YEPD medium in engineered S. cerevisiae.

Systems Bioengineering Laboratory

교수님 소개

오민규

연구실 소개

연구실 키워드

알럼나이가 간 회사

연구실 지원 방법

대우 조건

연도별 논문 인용수

저널 & 학회 논문 출판 수

연구실 논문 목록

Applications and advances in bioelectronic noses for odour sensing

Characterization of poly-3-hydroxybutyrate (PHB) produced from Ralstonia eutropha using an alkali-pretreated biomass feedstock

A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae

연구실 보유 특허

대학별 입시끈

우리 연구실 모집

교수님 소개

오민규

연구실 키워드

알럼나이가 간 회사

연구실 지원 방법

대우 조건

연도별 논문 인용수

저널 & 학회 논문 출판 수

연구실 논문 목록

Applications and advances in bioelectronic noses for odour sensing

Characterization of poly-3-hydroxybutyrate (PHB) produced from Ralstonia eutropha using an alkali-pretreated biomass feedstock

A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae

연구실 보유 특허

최근 3년간 연구실적 높은 연구실

대학별 입시끈

우리 연구실 모집