A5060226532- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Gut microbiota and health
- Biofuel production and bioconversion
- Diet and metabolism studies
- Gene Regulatory Network Analysis
- Bacteriophages and microbial interactions
- Bacterial biofilms and quorum sensing
- Microbial Natural Products and Biosynthesis
- Evolution and Genetic Dynamics
- Clostridium difficile and Clostridium perfringens research
- Frailty in Older Adults
- Vibrio bacteria research studies
- Advanced biosensing and bioanalysis techniques
- Antibiotic Resistance in Bacteria
- Microbial Metabolism and Applications
- DNA and Biological Computing
- Cancer Research and Treatments
- Viral Infectious Diseases and Gene Expression in Insects
- Ubiquitin and proteasome pathways
- Microbial Community Ecology and Physiology
- Gene expression and cancer classification
Korea Advanced Institute of Science and Technology
2014-2025
La Jolla Bioengineering Institute
2024
University of California, San Diego
2022-2024
Along with functional advances in the use of CRISPR/Cas9 for genome editing, endonuclease-deficient Cas9 (dCas9) has provided a versatile molecular tool exploring gene functions. In principle, differences cell phenotypes that result from RNA-guided modulation transcription levels by dCas9 are critical inferring function; however, effect intracellular expression on bacterial morphology not been systematically elucidated. Here, we observed unexpected morphological changes Escherichia coli...
Abstract Synthetic biology aims to design and construct bacterial genomes harboring the minimum number of genes required for self-replicable life. However, genome-reduced bacteria often show impaired growth under laboratory conditions that cannot be understood based on removed genes. The unexpected phenotypes highlight our limited understanding genomes. Here, we deploy adaptive evolution (ALE) re-optimize performance a strain. basis suboptimal is imbalanced metabolism rewired during ALE....
The gut microbiota is associated with diverse age-related disorders. Several rejuvenation methods, such as probiotic administration and faecal transplantation, have been applied to alter the microbiome promote healthy ageing. Nevertheless, prolongation of health span aged mice by remodelling remains challenging.Here, we report changes in microbial communities their functions mouse models during ageing three procedures including co-housing, serum-injection parabiosis. Our results showed that...
Abstract Machine learning applied to large compendia of transcriptomic data has enabled the decomposition bacterial transcriptomes identify independently modulated sets genes, such iModulons represent specific cellular functions. The identification enables accurate genes necessary and sufficient for cross-species transfer We demonstrate of: 1) biotransformation vanillate protocatechuate, 2) a malonate catabolic pathway, 3) pathway 2,3-butanediol, 4) an antimicrobial resistance ampicillin...
RNA sequencing techniques have enabled the systematic elucidation of gene expression (RNA-Seq), transcription start sites (differential RNA-Seq), transcript 3′ ends (Term-Seq), and post-transcriptional processes (ribosome profiling). The main challenge transcriptomic studies is to remove ribosomal RNAs (rRNAs), which comprise more than 90% total in a cell. Here, we report low-cost robust bacterial rRNA depletion method, RiboRid, based on enzymatic degradation by thermostable RNase H. This...
Pyruvate is an important intermediate of central carbon metabolism and connects a variety metabolic pathways in Escherichia coli Although the intracellular pyruvate concentration dynamically altered tightly balanced during cell growth, transport system remains unclear. Here, we identified transporter E. using high-throughput transposon sequencing. The mutant library (a total 5 × 105 mutants) was serially grown with toxic analog (3-fluoropyruvate [3FP]) to enrich for mutants lacking function....
Staphylococcus aureus infection is a rising public health care threat. S. believed to have elaborate regulatory networks that orchestrate its virulence. Despite importance, the systematic understanding of transcriptional landscape limited. Here, we describe primary transcriptome an epidemic USA300 isolate community-acquired methicillin-resistant aureus. We experimentally determined 1,861 transcription start sites with their principal promoter elements, including well-conserved -35 and -10...
Adaptive laboratory evolution (ALE) is used to find causal mutations that underlie improved strain performance under the applied selection pressure. ALE studies have revealed mutator populations tend outcompete their non-mutator counterparts following evolutionary trajectory. Among them, mutS-inactivated cells, characterized by a dysfunctional methyl-mismatch repair system, are frequently found in experiments. Here, we examined mutS inactivation as an approach facilitate of Escherichia coli....
iModulons-sets of co-expressed genes identified through independent component analysis (ICA) high-quality transcriptomic datasets-provide an unbiased, modular view organism's transcriptional regulatory network. Established in 2020, iModulonDB (iModulonDB.org) serves as a centralized repository curated iModulon sets, enabling users to explore iModulons and download the associated data. This update reflects significant expansion database-19 new ICA decompositions (+633%) spanning 8 925...
As the design of genetic circuitry for synthetic biology becomes more sophisticated, diverse regulatory bioparts are required. Despite their importance, well-characterized 3'-untranslated region (3'-UTR) limited. Thus, transcript 3'-ends require further investigation to understand underlying role and applications 3'-UTR. Here, we revisited use Term-Seq in Escherichia coli strain K-12 MG1655 enhance our understanding 3'-UTR functions provide a collection tunable with wide termination strength...
A genome contains the information underlying an organism's form and function. Yet, we lack formal framework to represent study this information. Here, introduce Bitome, a matrix composed of binary digits (bits) representing genomic positions features. We Bitome for Escherichia coli K-12 MG1655. find that: (i) features are encoded unevenly, both spatially categorically; (ii) coding intergenic recapitulated at high resolution; (iii) adaptive mutations skewed towards with fewer features; (iv)...
Streptomyces sp. is a great source of bioactive secondary metabolites, including antibiotics, antifungal agents, antiparasitic immunosuppressant compounds, and other drugs. Secondary metabolites are synthesized via multistep conversions the precursor molecules from primary metabolism, governed by multicomplex enzymes metabolite biosynthetic gene clusters.
Flavin mononucleotide (FMN)-based fluorescent proteins are versatile reporters that can monitor various cellular processes in both aerobic and anaerobic conditions. However, the understanding of role individual amino acid residues on protein function has been limited restricted development better functional variants. Here we examine Escherichia coli flavin binding (EcFbFP) using application high-throughput sequencing variants, termed deep mutational scanning. The variants were classified...
Abstract Streptomyces produces diverse secondary metabolites of biopharmaceutical importance, yet the rate biosynthesis these is often hampered by complex transcriptional regulation. Therefore, a fundamental understanding regulation in key to fully harness its genetic potential. Here, independent component analysis (ICA) 454 high‐quality gene expression profiles model species coelicolor performed, which 249 are newly generated for S. cultivated on 20 different carbon sources and 64...