Sang Yup Lee

Korea Advanced Institute of Science and Technology | KAIST · Department of Chemical and Biomolecular Engineering

Background Oncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells. Identification of such mutation-associated metabolites will facilitate developing treatment strategies for cancers, but is challenging due to a large number of metabolites in a cell and the presence of...

CRISPR tools, especially Cas9n-sgRNA guided cytidine deaminase base editors such as CRISPR-BEST, have dramatically simplified genetic manipulation of streptomycetes. One major advantage of CRISPR base editing technology is the possibility to multiplex experiments in genomically instable species. Here, we demonstrate scaled up Csy4 based multiplexed...

Valerolactam (VL) is an important precursor chemical for nylon-5 and nylon 6,5. It has been produced by petroleum-based route involving harsh reaction conditions and generating toxic wastes. Here we report the complete biosynthesis of VL by metabolically engineered Corynebacterium glutamicum overproducing L-lysine. The pathway comprising L-lysine m...

Escherichia coli has been employed as a workhorse for the efficient production of recombinant proteins. However, some proteins were found to be difficult to produce in E. coli. The stability of mRNA has been considered as one of the important factors affecting recombinant protein production. Here we report a generally applicable and simple strategy...

Synthetic sRNAs allow knockdown of target genes at translational level, but have been restricted to a limited number of bacteria. Here, we report the development of a broad-host-range synthetic sRNA (BHR-sRNA) platform employing the RoxS scaffold and the Hfq chaperone from Bacillus subtilis. BHR-sRNA is tested in 16 bacterial species including comm...

Here, we report the construction of a Clostridium acetobutylicum strain ATCC 824 (pCD07239) by heterologous expression of carbonyl branch genes (CD630_0723∼CD630_0729) from Clostridium difficile, aimed at installing a heterologous Wood-Ljungdahl pathway (WLP). As part of this effort, in order to validate the methyl branch of the WLP in the C. aceto...

Pfizer's Paxlovid has recently been approved for the emergency use authorization (EUA) from the US Food and Drug Administration (FDA) for the treatment of mild-to-moderate COVID-19. Drug interactions can be a serious medical problem for COVID-19 patients with underlying medical conditions, such as hypertension and diabetes, who have likely been tak...

Terephthalic acid (TPA) is an important commodity chemical used as a monomer of polyethylene terephthalate (PET). Since a large quantity of PET is routinely manufactured and consumed worldwide, the development of sustainable biomanufacturing processes for its monomers (i.e. TPA and ethylene glycol) has recently gained much attention. In a previous...

Bio-based production of chemicals and materials has attracted much attention due to the urgent need to establish sustainability and enhance human health. Metabolic engineering (ME) allows purposeful modification of cellular metabolic, regulatory, and signaling networks to achieve enhanced production of desired chemicals and degradation of environme...

Sustainable production of chemicals and materials from renewable non-food biomass using biorefineries has become increasingly important in an effort toward the vision of ‘net zero carbon’ that has recently been pledged by countries around the world. Systems metabolic engineering has allowed the efficient development of microbial strains overproduci...

Increased awareness of the environmental and health concerns of consuming chemically synthesized products has led to a rising demand for natural products that are greener and more sustainable. Despite their importance, however, industrial-scale production of natural products has been challenging due to the low yield and high cost of the bioprocesse...

Microbial production of various TCA intermediates and related chemicals through the reductive TCA cycle has been of great interest. However, rumen bacteria that naturally possess strong reductive TCA cycle have been rarely studied to produce these chemicals, except for succinic acid, due to their dependence on fumarate reduction to transport electr...

Reducing atmospheric loads of greenhouse gases (GHGs), especially CO2 and CH4, has been considered the key to alleviating global crises we are facing, such as climate change, sea level elevation, and ocean acidification. To this end, development of strategies and technologies for carbon capture, sequestration, and utilization (CCSU) is urgently nee...

The sustainable production of chemicals from renewable, nonedible biomass has emerged as an essential alternative to address pressing environmental issues arising from our heavy dependence on fossil resources. Microbial cell factories are engineered microorganisms harboring biosynthetic pathways streamlined to produce chemicals of interests from re...

Phages are regarded as powerful antagonists of bacteria, especially in industrial fermentation processes involving bacteria. While bacteria have developed various defense mechanisms, most of which are effective against a narrow range of phages and consequently exert limited protection from phage infection. Here, we report a strategy for developing...

The biosynthesis of natural products often requires eukaryotic cytochrome P450s (P450s) in combination with P450 reductase, in physical proximity, to perform electron-transfer reactions. Unfortunately, functional expression of eukaryotic P450s in bacteria remains generally difficult. Here we report an electron channelling strategy based on the appl...

Metabolic engineering for the bio-based production of chemicals requires thorough understanding of metabolic reactions including enzymes, cofactors, reactants, and products. Here we present an interactive bio-based chemicals map that visualizes compounds, enzymes, and reaction pathways together with strategies for the production of chemicals by bio...

Heme has recently attracted much attention due to its promising applications in food and healthcare industries. However, the current titers and productivities of heme produced by recombinant microorganisms are not high enough for a wide range of applications. In this study, the process for the fermentation of the metabolically engineered E. coli HA...

Zinc protoporphyrin IX (ZnPPIX) has been considered as a promising red colorant for food industries as well as an anti‐cancer drug. However, bio‐based production of ZnPPIX from a renewable carbon source has not been reported yet. In this study, a fermentation process of the metabolically engineered E. coli HAEM7 strain was optimized for the high‐le...

There is an evergrowing demand for environment-friendly processes to synthesize ammonia (NH3) from atmospheric nitrogen (N2). Although diazotrophic N2 fixation represents an undeniably "green" process of NH3 synthesis, the slow reaction rate makes it less suitable for industrially meaningful large-scale production. Here, we report the photoinduced...

Synthetic colorants have predominated over natural colorants mainly due to their relatively more stable color, larger synthesis scale, and lower manufacturing costs. However, the environmental and health impacts arising from the excess use of these chemicals have brought up increasing demand for natural colorants. Recent advances in microbial metab...

Utilization of CO2 by converting it to useful organic compounds is an important strategy to move toward carbon neutrality and sustainable societies. Biological systems including plants and algae have driven conversion of CO2 to diverse organic compounds using their CO2 assimilation pathways and reducing powers. In this article, metabolic pathways a...

Chemical induction is one of the most common modalities used to manipulate gene expression in living systems. However, chemical induction can be toxic or expensive that compromise the economic feasibility when it comes to industrial-scale synthetic biology applications. These complications have driven the pursuit of better induction systems. Optoge...

Metabolic engineering for developing industrial strains capable of overproducing bioproducts requires good understanding of cellular metabolism, including metabolic reactions and enzymes. However, metabolic pathways and enzymes involved are still unknown for many products of interest, which presents a key challenge in their biological production. T...

Recombinant Escherichia coli (E. coli) strain that produces phytochelatin (PC) and/or metallothionein (MT) can synthesize various metal nanoparticles (NPs) by reducing metal ions. Here we report in vivo biosynthesis of iron oxide nanocomposites (NCs) using recombinant E. coli. We designed a strategy of biosynthesizing iron oxide NCs by first intern...

Spider dragline silk is a remarkable fiber made of unique proteins—spidroins—secreted and stored as a concentrated aqueous dope in the major ampullate gland of spiders. This feat has inspired engineering of microbes to secrete spidroins for spinning into tough synthetic fibers, which remains a challenge due to the aggregation-prone feature of the s...

ATPase, a key enzyme involved in energy metabolism, has not yet been well studied in Clostridium acetobutylicum . Here, we knocked down the atpG gene encoding the ATPase gamma subunit in C. acetobutylicum ATCC 824 using a mobile group II intron system and analyzed the physiological characteristics of the atpG gene knockdown mutant, 824-2866KD. Prop...

Streptomyces griseofuscus DSM 40191 is a fast growing Streptomyces strain that remains largely underexplored as a heterologous host. Here, we report the genome mining of S. griseofuscus, followed by the detailed exploration of its phenotype, including the production of native secondary metabolites and ability to utilise carbon, nitrogen, sulphur an...

CRISPR base editing is a powerful method to engineer bacterial genomes. However, it restricts editing to single-nucleotide substitutions. Here, to address this challenge, we adapt a CRISPR-Prime Editing-based, DSB-free, versatile, and single-nucleotide resolution genetic manipulation toolkit for prokaryotes. It can introduce substitutions, deletion...

Sustainable food production is a key to solve complicated and intertwined issues of overpopulation, climate change, environment and sustainability. Microorganisms, which have been routinely consumed as a part of fermented foods and more recently as probiotic dietary supplements, can be repurposed for our food to present a sustainable solution to cu...

Significance Recent spread of SARS-CoV-2 has sparked significant health concerns of emerging infectious viruses. Drug repurposing is a tangible strategy for developing antiviral agents within a short period. In general, drug repurposing starts with virtual screening of approved drugs employing docking simulations. However, the actual hit rate is lo...

In article number 2100743, Dongsoo Yang, Seon Young Park, and Sang Yup Lee report the microbial production of proviolacein, prodeoxyviolacein, violacein, and deoxyviolacein as natural green, blue, navy, and purple colorants, in addition to astaxanthin, β‐carotene, and zeaxanthin known to be red, orange, and yellow colorants. Integration of systems...

Metabolic engineering has become an essential technology for developing microbial cell factories for producing chemicals and materials from sustainable and renewable feedstocks. Equipped with the ever‐advancing tools and strategies of modern systems biology and synthetic biology, traditional metabolic engineering has been upgraded to a next and sys...

There has been much interest in producing natural colorants to replace synthetic colorants of health concerns. Escherichia coli has been employed to produce natural colorants including carotenoids, indigo, anthocyanins, and violacein. However, production of natural green and navy colorants has not been reported. Many natural products are hydrophobi...

Bio-based production of industrially important chemicals and materials from non-edible and renewable biomass has become increasingly important to resolve the urgent worldwide issues including climate change. Also, bio-based production, instead of chemical synthesis, of food ingredients and natural products has gained ever increasing interest for he...

The use of CO2 as a carbon source in biorefinery is of great interest, but the low solubility of CO2 in water and the lack of efficient CO2 assimilation pathways are challenges to overcome. Formic acid (FA), which can be easily produced from CO2 and more conveniently stored and transported than CO2, is an attractive CO2‐equivalent carbon source as...

Carminic acid is an aromatic polyketide found in scale insects (i.e., Dactylopius coccus) and is a widely used natural red colorant. It has long been produced by the cumbersome farming of insects followed by multistep purification processes. Thus, there has been much interest in producing carminic acid by the fermentation of engineered bacteria. He...

ε-poly-L-lysine is a potent antimicrobial produced through fermentation of Streptomyces and used in many Asian countries as a food preservative. It is synthesized and excreted by a special NRPS-like enzyme called Pls. Here we discovered a gene from cheese bacterium Corynebacterium variabile that showed high similarity to the Pls from Streptomyces i...

Genome-scale metabolic modeling and simulation have been widely employed in biological studies and biotechnological applications due to their poweful capabilities of estimating metabolic fluxes at systems level. In recent years, machine learning (ML) has been beginning to be applied to the reconstruction and analysis of genome-scale metabolic model...

Technical universities are constantly experimenting with innovative student-centred classroom approaches. We describe flipped and linked classroom approaches in the context of our ongoing chemical education theme of catalysis.

Significance Identification of transcription factors (TFs) is a starting point for the analysis of transcriptional regulatory systems of organisms. Here, we report the development of DeepTFactor, a deep learning-based tool that predicts TFs using protein sequences as inputs. We interpreted the reasoning process of DeepTFactor, confirming that DeepT...

Bio-based production of many chemicals is not yet possible due to the unknown biosynthetic pathways. Here, we report a strategy combining retrobiosynthesis and precursor selection step to design biosynthetic pathways for multiple short-chain primary amines (SCPAs) that have a wide range of applications in chemical industries. Using direct precursor...

Retrobiosynthesis allows the designing of novel biosynthetic pathways for the production of chemicals and materials through metabolic engineering but generates a large number of reactions beyond the experimental feasibility. Thus, an effective method that can reduce a large number of the initially predicted enzymatic reactions has been needed. Here...

Exacerbation of climate change and air pollution around the world have emphasized the necessity of replacing fossil fuels with clean and sustainable energy. Metabolic engineering has provided strategies to engineer diverse organisms for the production of biofuels from renewable carbon sources. Although some of the processes are commercialized, ther...

We engineered Escherichia coli to grow on CO2 and formic acid alone by introducing the synthetic CO2 and formic acid assimilation pathway, expressing two formate dehydrogenase genes, fine-tuning metabolic fluxes and optimizing the levels of cytochrome bo3 and bd-I ubiquinol oxidase. Our engineered strain can grow to an optical density at 600 nm of...

Non-ribosomal peptides (NRPs) are a family of secondary metabolites with the highest number among entire secondary metabolite types. They are biosynthesized by a multi-modular enzyme complex called non-ribosomal peptide synthetase (NRPS), which is encoded by a biosynthetic gene cluster (BGC) in plants and a special group of microorganisms. NRPs are...

Phenylpropanoids are a group of diverse natural products derived from aromatic amino acids. Although their demands are high both as drugs and nutraceuticals, their production mainly depends on inefficient extraction from plants. To achieve sustainable production of phenylpropanoids, engineering model microorganisms such as Escherichia coli has been...

Affordable and automated cloning platforms are essential to many synthetic biology studies. However, the traditional E. coli-based cloning is a major bottleneck as it requires heat shock or electroporation implemented in the robotic workflows. To overcome this problem, we explored bacterial natural transformation for automatic DNA cloning and engin...

Fine control of the expression levels of proteins constitutes a major challenge in synthetic biology and metabolic engineering. However, the dependence of translation initiation on the downstream coding sequence (CDS) obscures accurate prediction of the protein expression levels from mRNA sequences. Here, we present a tunable gene-expression system...

Significance Glutaric acid is an important dicarboxylic acid used in the synthesis of commercial polymers. Here we report metabolic engineering of an l -lysine–overproducing Corynebacterium glutamicum strain for the high-level production of glutaric acid. The glutaric acid biosynthesis pathway was established in C. glutamicum by optimally expressin...

Streptomyces griseofuscus DSM 40191 is a fast growing Streptomyces strain that remains largely underexplored as a heterologous host. Here, we report the genome mining of S. griseofuscus , followed by the detailed exploration of its phenotype, including production of native secondary metabolites and ability to utilise carbon, nitrogen, sulphur and p...

Benzoic acid (BA) is an important platform aromatic compound in chemical industry and is widely used as food preservatives in its salt forms. Yet, current manufacture of BA is dependent on petrochemical processes under harsh conditions. Here we report the de novo production of BA from glucose using metabolically engineered Escherichia coli strains...

Current understanding of heat shock response has been complicated by the fact that heat stress is inevitably accompanied by changes in specific growth rates and growth stages. In this study, a chemostat culture was successfully performed to avoid the physico-chemical and biological changes that accompany heatshock, which provided a unique opportuni...

Inorganic nanomaterials are widely used in chemical, electronics, photonics, energy and medical industries. Preparing a nanomaterial (NM) typically requires physical and/or chemical methods that involve harsh and environmentally hazardous conditions. Recently, wild-type and genetically engineered microorganisms have been harnessed for the biosynthe...

Microbial production of fatty acids and derivatives from non-edible biomass has attracted much attention as an alternative to their production from plant oils and animal fats. Fatty acids and some of their derivatives are ubiquitous metabolites synthesized for membrane biosynthesis and other metabolic purposes in microorganisms. These compounds, ho...

Systems metabolic engineering attempts to engineer a production host’s biological network to overproduce valuable chemicals and materials in a sustainable manner. In contrast to genome-scale metabolic models that are well established, regulatory network models have not been sufficiently considered in systems metabolic engineering despite their impo...

Membraneless organelles formed by liquid–liquid phase separation of proteins or nucleic acids are involved in diverse biological processes in eukaryotes. However, such cellular compartments have yet to be discovered or created synthetically in prokaryotes. Here, we report the formation of liquid protein condensates inside the cells of prokaryotic E...

In most prokaryotes, missing and poorly active non-homologous end joining (NHEJ) DNA repair pathways heavily restrict the direct application of CRISPR-Cas for DNA double-strand break (DSB)-based genome engineering without providing editing templates. CRISPR base editors, on the other hand, can be directly used for genome engineering in a number of...

Polyhydroxyalkanoates (PHAs) are a family of polyesters synthesized and intracellularly accumulated as distinct granules in many microorganisms. PHAs are promising materials to substitute the petroleum‐based plastics currently in use. In article 1907138, Sang Yup Lee and co‐workers provide a comprehensive overview of PHAs, including their biosynthe...

Epsilon-polylysine (ε-PL) is an antimicrobial commercially produced by Streptomyces fermentation and widely used in Asian countries for food preservation. Here we discovered a gene from cheese bacterium Corynebacterium variabile that showed high similarity to the ε-PL synthetase from Streptomyces in terms of enzymatic domain architecture and gene c...

Just as World War II ushered in a new era reset on the foundations of science and innovation, COVID-19 has opened up new potentials to transform the world based on the Fourth Industrial Revolution (4IR). The ability to make most of the new technological potentials will be critical to build robust, sustainable, inclusive, and competitive economies i...

Bacterial cellulose (BC) has outstanding physical and chemical properties, including high crystallinity, moisture retention, and tensile strength. Currently, the major producer of BC is Komagataeibacter xylinus. However, due to limited tools of expression, this host is difficult to engineer metabolically to improve BC productivity. In this study, a...

Streptomycetes are prominent sources of bioactive natural products, but metabolic engineering of the natural products of these organisms is greatly hindered by relatively inefficient genetic manipulation approaches. New advances in genome editing techniques, particularly CRISPR-based tools, have revolutionized genetic manipulation of many organisms...

Sustainable production of chemicals from renewable non-food biomass has become a promising alternative to overcome environmental issues caused by our heavy dependence on fossil resources. Systems metabolic engineering, which integrates traditional metabolic engineering with systems biology, synthetic biology, and evolutionary engineering, is enabli...

4‐Amino‐1‐butanol (4AB) serves as an important intermediate compound for drugs and a precursor of biodegradable polymers used for gene delivery. Here, we report for the first time the fermentative production of 4AB from glucose by metabolically engineered Corynebacterium glutamicum harboring a newly designed pathway comprising a putrescine aminotra...

Succinic acid (SA), a dicarboxylic acid of industrial importance, can be efficiently produced by metabolically engineered Mannheimia succiniciproducens. Malate dehydrogenase (MDH) is one of the key enzymes for SA production, but has not been well characterized. Here we report biochemical and structural analyses of various MDHs and development of hy...

Poly(d‐lactate‐co‐glycolate‐co‐4‐hydroxybutyrate) [poly(d‐LA‐co‐GA‐co‐4HB)] and poly(d‐lactate‐co‐glycolate‐co‐4‐hydroxybutyrate‐co‐d‐2‐hydroxybutyrate) [poly(d‐LA‐co‐GA‐co‐4HB‐co‐d‐2HB)] are of interest for their potential applications as new biomedical polymers. Here we report their enhanced production by metabolically engineered Escherichia coli...