A5066692256- Microbial Metabolic Engineering and Bioproduction
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- Gene Regulatory Network Analysis
- CRISPR and Genetic Engineering
- Enzyme Catalysis and Immobilization
- Biofuel production and bioconversion
- Viral Infectious Diseases and Gene Expression in Insects
- Silicon Nanostructures and Photoluminescence
- Amino Acid Enzymes and Metabolism
- Graphene research and applications
- Advanced biosensing and bioanalysis techniques
- Cancer Research and Treatments
- Enzyme Structure and Function
- Nanowire Synthesis and Applications
- Enzyme Production and Characterization
- Nanopore and Nanochannel Transport Studies
- Microfluidic and Capillary Electrophoresis Applications
- Photosynthetic Processes and Mechanisms
- Bacteriophages and microbial interactions
- RNA Interference and Gene Delivery
- Microfluidic and Bio-sensing Technologies
- RNA modifications and cancer
- RNA Research and Splicing
- Chemical Synthesis and Analysis
Seoul National University
2016-2025
Yonsei University
2025
KG Chemical (South Korea)
2023
City College of New York
2022
University of California, San Diego
2014-2020
La Jolla Bioengineering Institute
2020
Kyung Hee University
2017-2018
Seoul Institute
2018
Government of the Republic of Korea
2018
Yong In University
2017
Highlights•Genome-wide reconstruction of OxyR, SoxR, and SoxS regulons in E. coli•68 genes 51 TUs belong to these regulons, 48 are directly regulated•Regulatory roles include direct activation amino acid biosynthesis•Roles also cell wall synthesis divalent metal ion transportSummaryThree transcription factors (TFs), SoxS, play a critical role transcriptional regulation the defense system for oxidative stress bacteria. However, their full genome-wide regulatory potential is unknown. Here, we...
Catalysis using iron-sulfur clusters and transition metals can be traced back to the last universal common ancestor. The damage metalloproteins caused by reactive oxygen species (ROS) prevent cell growth survival when unmanaged, thus eliciting an essential stress response that is fundamental in biology. Here we develop a computable multiscale description of ROS Escherichia coli, called OxidizeME. We use OxidizeME explain four key responses oxidative stress: 1) ROS-induced auxotrophy for...
Abstract Transcriptional regulation enables cells to respond environmental changes. Of the estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 have been experimentally identified, but ChIP methods used fully characterize only a few dozen. Identifying these remaining TFs is key improving our knowledge of E. transcriptional regulatory network (TRN). Here, we developed an integrated workflow for computational prediction and comprehensive experimental...
The regulators GadE, GadW and GadX (which we refer to as GadEWX) play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system Escherichia coli K-12 MG1655. However, genome-wide regulatory GadEWX is still unknown. Here comprehensively reconstruct network RpoS involvement E. MG1655 under acidic stress. Integrative data analysis reveals that regulons consist 45 genes 31 transcription units 28 these were associated with RpoS-binding sites. We...
Two major transcriptional regulators of carbon metabolism in bacteria are Cra and CRP. CRP is considered to be the main mediator catabolite repression. Unlike for CRP, vivo DNA binding information scarce. Here we generate integrate ChIP-exo RNA-seq data identify 39 sites 97 regulon genes that regulated by Escherichia coli. An integrated metabolic-regulatory network was formed including experimentally-derived regulatory a genome-scale metabolic reconstruction. Applying analysis methods...
Control of enzyme allosteric regulation is required to drive metabolic flux toward desired levels. Although the three-dimensional (3D) structures many enzyme-ligand complexes are available, it still difficult rationally engineer an allosterically regulatable without decreasing its catalytic activity. Here, we describe effective strategy deregulate inhibition enzymes based on molecular evolution and physicochemical characteristics ligand-binding sites. We found that sites evolutionarily...
Butyrate pathway was constructed in recombinant Escherichia coli using the genes from Clostridium acetobutylicum and Treponema denticola. However, exogenous enzymes did not efficiently convert carbon flux to butyrate. Three steps of productivity enhancement were attempted this study. First, engineering delete metabolic pathways by-products successfully improved butyrate production. Second, synthetic scaffold protein that spatially co-localizes introduced improve efficiency heterologous...
Semitransparent flexible photovoltaic cells are advantageous for effective use of solar energy in many areas such as building-integrated solar-power generation and portable chargers. We report semitransparent organic (FOSCs) with high aperture, composed doped graphene layers, ZnO, P3HT:PCBM, PEDOT:PSS anode/cathode transparent conductive electrodes (TCEs), electron transport layer, photoactive hole respectively, fabricated based on simple solution processing. The FOSCs do not only harvest...
Abstract Balancing the amounts of enzymes is one important factors to achieve optimum performance a designed metabolic pathway. However, random mutagenesis approach impractical since it requires searching an unnecessarily large number variants and often results in narrow range expression levels which are out optimal level. Here, we developed predictive combinatorial design method, called UTR Library Designer, systematically searches space levels. It accomplishes this by designing synthetic...
Abstract Although brown macroalgae holds potential as an alternative feedstock, its utilization by conventional microbial platforms has been limited due to the inability metabolize one of principal sugars, alginate. Here, we isolate Vibrio sp. dhg, a fast-growing bacterium that can efficiently assimilate Based on systematic characterization genomic information establish genetic toolbox for engineering. We also demonstrate ability rapidly produce ethanol, 2,3-butanediol, and lycopene from...
The-state-of-the-art bio- and nanotechnology have opened up an avenue to noninvasive liquid biopsy for identifying diseases from biomolecules in bloodstream, especially DNA. In this work, we combined sequence-specific-labeling scheme using mutated clustered regularly interspaced short palindromic repeats associated protein 9 without endonuclease activity (CRISPR/dCas9) ion concentration polarization (ICP) phenomenon as a mechanism selectively preconcentrate targeted DNA molecules rapid...
Abstract Precise control of gene expression is essential for flux redistribution in metabolic pathways. Although the CRISPR interference (CRISPRi) system can effectively repress at transcriptional level, it has still been difficult to precisely level without loss specificity or an increase cell toxicity. In this study, we developed a tunable CRISPRi that performs regulation various levels. We constructed single-guide RNA (sgRNA) library targeting repeat, tetraloop, and anti-repeat regions...
Abstract Biodegradable polymer/ceramic composite scaffold could overcome limitations of biodegradable polymers or ceramics for bone regeneration. Injectable has raised great interest regeneration in vivo , since it allows one easy filling irregularly shaped defects and implantation osteogenic cells through minimally invasive surgical procedures The purpose this study was to determine whether apatite‐coated poly(lactic‐ co ‐glycolic acid) (PLGA) microspheres be used as an injectable...