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A KAIST team develops the world's first modular co-culture platform for the one-pot production of rainbow-colored bacterial cellulose.
<(From Left) Distinguished Professor Sang Yup Lee, Ph.D candidate Pingxin Lin, Ph.D candiate Zhou Hengrui>
The integration of systems metabolic engineering with co-culture strategies that couples bacterial cellulose production with natural colorant biosynthesis enabled the one-pot generation of rainbow-colored bacterial cellulose, establishing a sustainable biomanufacturing platform that can replace petroleum-based textiles and eliminate chemical dyeing processes.
A research group at KAIST has successfully developed a modular co-culture platform for the one-pot production of rainbow-colored bacterial cellulose. The team, led by Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering, engineered Komagataeibacter xylinus for bacterial cellulose synthesis and Escherichia coli for natural colorants overproduction. A co-culture of these engineered strains enabled the in situ coloration of bacterial cellulose. This research offers a versatile platform for producing living materials in multiple colors, and provides new opportunities for sustainable textiles, wearable biomaterials, and functional living materials that combine optical and structural properties beyond the reach of conventional textile technologies.
Bacterial cellulose is an attractive and biodegradable alternative to petroleum-derived fabrics due to its high purity, mechanical strength, and water-retention properties. However, the limited color range of bacterial cellulose, which is typically white, has limited its broader application in the textile industry, where more vibrant colored fabrics are increasingly desired. Conventional dyeing methods rely on petroleum-based colorants and toxic reagents, creating environmental and processing challenges. These challenges have driven the demand for alternative production methods.
To address these issues, KAIST researchers, including Ph.D. Candidate Hengrui Zhou, Ph.D. Candidate Pingxin Lin, Professor Ki Jun Jeong, and Distinguished Professor Sang Yup Lee, combined systems metabolic engineering with co-culture strategies to develop a bio-based route that integrates bacterial cellulose formation with natural pigment synthesis, enabling the production of colored living materials in a single step without additional chemical processing.
The team’s work, entitled “One-pot production of colored bacterial cellulose,” was published in Trends in Biotechnology on November 12,2025.
This research details the one-pot production of multicolored bacterial cellulose using a modular co-culture platform that integrates a bacterial cellulose-overproducing K. xylinus strain with natural colorant-producing E. coli strains. The team focused on addressing the limitations in bacterial cellulose coloration caused by environmental challenges and complex processing requirements. By employing vesicle engineering and optimizing co-culture parameters, the researchers achieved one-pot production of red, orange, yellow, green, blue, navy, and purple bacterial cellulose, eliminating the need for external dyes and toxic chemical treatments.
To enhance dyeing efficiency, E. coli strains were engineered for the overproduction and secretion of natural colorants. It was determined that the intracellular accumulation of these pigments disrupts cellular metabolism and physiology, thereby inhibiting their production. To overcome this limitation, vesicle engineering has emerged as a key strategy to mitigate these cytotoxic effects, including the induction of inner- and outer-membrane vesicles and the modulation of cell morphology, enabling the more efficient secretion of colorants and increased overall production. The engineered E. coli strains were optimized in fed-batch fermentation, achieving record-breaking production of 16.92 ± 0.10 g/L of deoxyviolacein, 8.09 ± 0.17 g/L of violacein, 1.82 ± 0.07 g/L of proviolacein, and 936.25 ± 9.70 mg/L of prodeoxyviolacein, the highest reported titers to date for all four violacein derivatives.
< Figure 1. Rainbow-colored bacterial cellulose (microbial fiber) with applied color >
A co-culture platform combining the K. xylinus with E. coli strains was further developed and optimized, enabling the in situ one-pot coloration of bacterial cellulose in vibrant green, blue, navy, and purple. Fed-batch fermentation further improved the performance of the platform, achieving the world-first one-pot production of multicolored bacterial cellulose on a larger scale. To expand the bacterial cellulose color palette, engineered carotenoid-producing E. coli strains were incorporated, enabling the successful synthesis of red, orange, and yellow bacterial cellulose. This milestone demonstrates the potential of microbial fermentation as a sustainable alternative to petroleum-based textile processes.
“We can anticipate that this microbial cell factory-based one-pot production of rainbow-colored bacterial cellulose has the potential to replace current petroleum-based textile processes,” said Ph.D. Candidate Hengrui Zhou. “The systems metabolic engineering strategies developed in this study could be broadly applied for the production of diverse sustainable textiles, wearable biomaterials, and functional living materials that combine optical and structural properties beyond the capabilities of conventional textile technologies.” He added, “This platform reduces the environmental impact while greatly expanding design possibilities. Beyond serving as a proof-of-concept, this technology offers a promising route toward scalable, eco-friendly fabrics with in situ coloration. Its modular design allows the incorporation of diverse natural colorant pathways, enabling the creation of living materials in multiple colors.”
< Figure 2. Schematic of a microbe-based platform for one-step production of rainbow-colored bacterial cellulose >
“As demand for sustainable textiles and living materials continues to grow, we expect that the integrated biomanufacturing platform developed here will play a pivotal role in producing diverse functional biomaterials with additional design possibilities in a single step, without additional chemical processing,” explained Distinguished Professor Sang Yup Lee.
This work was supported by the Development of Next-generation Biorefinery Platform Technologies for Leading Bio-based Chemicals Industry project (2022M3J5A1056072) and the Development of Platform Technologies of Microbial Cell Factories for the Next-generation Biorefineries project (2022M3J5A1056117) from the National Research Foundation supported by the Korean Ministry of Science and ICT.
Source:
Hengrui Zhou (1st), Pingxin Lin (2nd), Ki Jun Jeong (3rd), and Sang Yup Lee (Corresponding). “One-pot production of colored bacterial cellulose”. Trends in Biotechnology (Published) doi: 10.1016/j.tibtech.2025.09.019
2025.11.19 View 869 -
Professor Sang Yup Lee Selected as IETI 'Laureate Distinguished Fellow'
<Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering>
Professor Sang Yup Lee of KAIST Department of Chemical and Biomolecular Engineering has been selected as a 'Laureate Distinguished Fellow,' the highest rank of fellow, by the International Engineering and Technology Institute (IETI).
Professor Lee is a globally renowned biotechnologist who has been leading research on the sustainable production of bio-based chemicals, and he received the 'ENI Award' in 2018. With this selection, he stands shoulder-to-shoulder with the world's top scholars, including recipients of the Nobel, Fields, and Turing Prizes.
IETI is an international academic organization established in Hong Kong in 2015 to promote innovation and international cooperation in the fields of engineering, technology, and science. Each year, the institute selects researchers with significant academic influence worldwide and appoints them into three grades: Laureate Distinguished Fellow, Distinguished Fellow, and Fellow. Professor Lee has been named to the most prestigious grade among these.
<IETI 2025 Fellow Selection Photo>
A total of 70 new fellows were selected in 2025. Among them, 14 individuals were named Laureate Distinguished Fellows, which includes recipients of top honors such as the Nobel, Fields, and Turing Prizes. Besides Professor Lee, this group includes Dudley Herschbach of Harvard University (Nobel Prize in Chemistry), Vint Cerf of Google (Turing Award), and Shigefumi Mori of Kyoto University (Fields Medal).
IETI stated that the selection process involved a rigorous five-step procedure: nomination, qualification review, document screening, expert voting, and final evaluation. It also expressed hope that the newly appointed fellows will demonstrate academic leadership in their respective research fields and contribute to global scientific and technological innovation and the promotion of international cooperation.
2025.11.10 View 567 -
Chemobiological Platform Enables Renewable Conversion of Sugars into Core Aromatic Hydrocarbons of Petroleum
<(From Left) Professor Sun Kyu Han, Ph.D candidate Tae Wan Kim, Professor Kyeong Rok Choi, Professor Sang Yup Lee>
With growing concerns over fossil fuel depletion and the environmental impacts of petrochemical production, scientists are actively exploring renewable strategies to produce essential industrial chemicals. A collaborative research team—led by Distinguished Professor Sang Yup Lee, Senior Vice President for Research, from the Department of Chemical and Biomolecular Engineering, together with Professor Sunkyu Han from the Department of Chemistry at the Korea Advanced Institute of Science and Technology (KAIST)—has developed an integrated chemobiological platform that converts renewable carbon sources such as glucose and glycerol into oxygenated precursors, which are subsequently deoxygenated in the same solvent system to yield benzene, toluene, ethylbenzene, and p-xylene (BTEX), which are fundamental aromatic hydrocarbons used in fuels, polymers, and consumer products.
<Figure 1. Schematic representation of the chemobiological synthesis of BTEX from glucose or glycerol in Escherichia coli>
From Sugars to Aromatic Hydrocarbons of Petroleum
The researchers designed four metabolically engineered strains of Escherichia coli, each programmed to produce a specific oxygenated precursor—phenol, benzyl alcohol, 2-phenylethanol, or 2,5-xylenol. These intermediates are generated through tailored genetic modifications, such as deletion of feedback-regulated enzymes, overexpression of pathway-specific genes, and introduction of heterologous enzymes to expand metabolic capabilities.
During fermentation, the products were continuously extracted into the organic solvent isopropyl myristate (IPM). Acting as a dual-function solvent, IPM not only mitigated the toxic effects of aromatic compounds on cell growth but also served directly as the reaction medium for downstream chemical upgrading. By eliminating the need for intermediate purification, solvent exchange, or distillation, this solvent-integrated system streamlined the conversion of renewable feedstocks into valuable aromatics.
Overcoming Chemical Barriers in An Unconventional Solvent
A central innovation of this work lies in adapting chemical deoxygenation reactions to function efficiently within IPM—a solvent rarely used in organic synthesis. Traditional catalysts and reagents often proved ineffective under these conditions due to solubility limitations or incompatibility with biologically derived impurities.
Through systematic optimization, the team established mild and selective catalytic strategies compatible with IPM. For example, phenol was successfully deoxygenated to benzene in up to 85% yield using a palladium-based catalytic system, while benzyl alcohol was efficiently converted to toluene after activated charcoal pretreatment of the IPM extract. More challenging transformations, such as converting 2-phenylethanol to ethylbenzene, were achieved through a mesylation–reduction sequence adapted to the IPM phase. Likewise, 2,5-xylenol derived from glycerol was converted to p-xylene in 62% yield via a two-step reaction, completing the renewable synthesis of the full BTEX spectrum.
A Sustainable, Modular Framework
Beyond producing BTEX, the study establishes a generalizable framework for integrating microbial biosynthesis with chemical transformations in a continuous solvent environment. This modular approach reduces energy demand, minimizes solvent waste, and enables process intensification—key factors for scaling up renewable chemical production.
The high boiling point of IPM (>300 °C) simplifies product recovery, as BTEX compounds can be isolated by fractional distillation while the solvent is readily recycled. Such a design is consistent with the principles of green chemistry and the circular economy, providing a practical alternative to fossil-based petrochemical processes.
Toward A Carbon-Neutral Future
Dr. Xuan Zou, the first author of this paper, explaind, “By coupling the selectivity of microbial metabolism with the efficiency of chemical catalysis, this platform establishes a renewable pathway to some of the most widely used building blocks in the chemical industry. Future efforts will focus on optimizing metabolic fluxes, extending the platform to additional aromatic targets, and adopting greener catalytic systems.”
In addition, Distinguished Professor Sang Yup Lee noted “As the global demand for BTEX and related chemicals continues to grow, this innovation provides both a scientific and industrial foundation for reducing reliance on petroleum-based processes. It marks an important step toward lowering the carbon footprint of the fuel and chemical sectors while ensuring a sustainable supply of essential aromatic hydrocarbons.”
This research was supported by the Development of Platform Technologies of Microbial Cell Factories for the Next-Generation Biorefineries Project (2022M3J5A1056117) and the Development of Advanced Synthetic Biology Source Technologies for Leading the Biomanufacturing Industry Project (RS-2024-00399424), funded by the National Research Foundation supported by the Korean Ministry of Science and ICT. This study was published in the latest issue of the Proceedings of the National Academy of Sciences of the United States of America (PNAS).
2025.10.13 View 1261 -
A KAIST Team Engineers a Microbial Platform for Efficient Lutein Production
<(From Left) Ph.D. Candidate Hyunmin Eun, Distinguished Professor Sang Yup Lee, , Dr. Cindy Pricilia Surya Prabowo>
The application of systems metabolic engineering strategies, along with the construction of an electron channeling system, has enabled the first gram-per-liter scale production of lutein from Corynebacterium glutamicum, providing a viable alternative to plant-derived lutein production.
A research group at KAIST has successfully engineered a microbial strain capable of producing lutein at industrially relevant levels. The team, led by Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering, developed a novel C. glutamicum strain using systems metabolic engineering strategies to overcome the limitations of previous microbial lutein production efforts. This research is expected to be beneficial for the efficient production of other industrially important natural products used in food, pharmaceuticals, and cosmetics.
Lutein is a xanthophyll carotenoid found in egg yolk, fruits, and vegetables, known for its role in protecting our eyes from oxidative stress and reducing the risk of macular degeneration and cataracts. Currently, commercial lutein is predominantly extracted from marigold flowers; however, this approach has several drawbacks, including long cultivation times, high labor costs, and inefficient extraction yields, making it economically unfeasible for large-scale production. These challenges have driven the demand for alternative production methods.
To address these issues, KAIST researchers, including Ph.D. Candidate Hyunmin Eun, Dr. Cindy Pricilia Surya Prabowo, and Distinguished Professor Sang Yup Lee, applied systems metabolic engineering strategies to engineer C. glutamicum, a GRAS (Generally Recognized As Safe) microorganism widely used in industrial fermentation. Unlike Escherichia coli, which was previously explored for microbial lutein production, C. glutamicum lacks endotoxins, making it a safer and more viable option for food and pharmaceutical applications.
The team’s work, entitled “Gram-per-litre scale production of lutein by engineered Corynebacterium,” was published in Nature Synthesis on 04 July , 2025.
This research details the high-level production of lutein using glucose as a renewable carbon source via systems metabolic engineering. The team focused on eliminating metabolic bottlenecks that previously limited microbial lutein synthesis. By employing enzyme scaffold-based electron channeling strategies, the researchers improved metabolic flux towards lutein biosynthesis while minimizing unwanted byproducts.
<Lutein production metabolic pathway engineering>
To enhance productivity, bottleneck enzymes within the metabolic pathway were identified and optimized. It was determined that electron-requiring cytochrome P450 enzymes played a major role in limiting lutein biosynthesis. To overcome this limitation, an electron channeling strategy was implemented, where engineered cytochrome P450 enzymes and their reductase partners were spatially organized on synthetic scaffolds, allowing more efficient electron transfer and significantly increasing lutein production.
The engineered C. glutamicum strain was further optimized in fed-batch fermentation, achieving a record-breaking 1.78 g/L of lutein production within 54 hours, with a content of 19.51 mg/gDCW and a productivity of 32.88 mg/L/h—the highest lutein production performance in any host reported to date. This milestone demonstrates the feasibility of replacing plant-based lutein extraction with microbial fermentation technology.
“We can anticipate that this microbial cell factory-based mass production of lutein will be able to replace the current plant extraction-based process,” said Ph.D. Candidate Hyunmin Eun. He emphasized that the integrated metabolic engineering strategies developed in this study could be broadly applied for the efficient production of other valuable natural products used in pharmaceuticals and nutraceuticals.
<Schematic diagram of microbial-based lutein production platform>
“As maintaining good health in an aging society becomes increasingly important, we expect that the technology and strategies developed here will play pivotal roles in producing other medically and nutritionally significant natural products,” added Distinguished Professor Sang Yup Lee.
This work is supported by the Development of Next-generation Biorefinery Platform Technologies for Leading Bio-based Chemicals Industry project 2022M3J5A1056072 and the Development of Platform Technologies of Microbial Cell Factories for the Next-Generation Biorefineries project 2022M3J5A1056117 from the National Research Foundation supported by the Korean Ministry of Science and ICT.
Source:
Hyunmin Eun (1st), Cindy Pricilia Surya Prabowo (co-1st), and Sang Yup Lee (Corresponding). “Gram-per-litre scale production of lutein by engineered Corynebacterium”. Nature Synthesis (Online published)
For further information:
Sang Yup Lee, Distinguished Professor of Chemical and Biomolecular Engineering, KAIST (leesy@kaist.ac.kr, Tel: +82-42-350-3930)
2025.07.14 View 3532 -
Distinguished Professor Sang Yup Lee Wins 2025 Global Metabolic Engineering Award
< Distinguished Professor Sang Yup Lee (Senior Vice President for Research) from the Department of Chemical & Biomolecular Engineering >
KAIST announced on the 20th that Professor Sang Yup Lee, who serves as the Vice President for Research and a Distinguished Professor at our university, has been awarded the '2025 Gregory N. Stephanopoulos Award for Metabolic Engineering' by the International Metabolic Engineering Society (IMES). Professor Lee delivered his award lecture at the 16th Metabolic Engineering Conference (ME16), held in Copenhagen, Denmark, from June 15th to 19th.
This award was established through contributions from the American Institute of Chemical Engineers (AIChE) Foundation, as well as fellow colleagues and acquaintances, to honor the achievements of Dr. Gregory Stephanopoulos, widely recognized as one of the pioneers of metabolic engineering. Presented biennially, the award recognizes scientists who have successfully commercialized fundamental research in metabolic engineering or have made outstanding contributions to the quantitative analysis, design, and modeling of metabolic pathways.
Professor Sang Yup Lee boasts an impressive record of over 770 journal papers and more than 860 patents. His groundbreaking research in metabolic engineering and biochemical engineering is highly acclaimed globally.
Throughout his 31 years as a professor at KAIST, Professor Lee has developed various metabolic engineering-based technologies and strategies. These advancements have been transferred to industries, facilitating the production of bulk chemicals, polymers, natural products, pharmaceuticals, and health functional foods. He has also founded companies and actively engages in advisory roles with various enterprises.
The International Metabolic Engineering Society (IMES) defines metabolic engineering as the manipulation of metabolic pathways in microorganisms or cells to produce useful substances (such as pharmaceuticals, biofuels, and chemical products). It utilizes tools like systems biology, synthetic biology, and computational modeling with the aim of enhancing the economic viability and sustainability of bio-based processes.
Furthermore, Professor Lee previously received the Merck Metabolic Engineering Award, a prominent international award in the field, in 2008. In 2018, he was honored with the Eni Award, often referred to as the Nobel Prize in energy, presented by the President of Italy.
Professor Sang Yup Lee remarked, "Metabolic engineering is a discipline that leads the current and future of biotechnology. It is a tremendous honor to receive this meaningful award at a time when the transition to a bio-based economy is accelerating. Together with my students and fellow researchers, we have generated numerous patents and transferred technologies to industry, and also established startups in the fields of biofuels, wound healing, and cosmetics. I will continue to pursue research that encompasses both fundamental research and technological commercialization."
The 'International Metabolic Engineering Society (IMES)' is a specialized society under the American Institute of Chemical Engineers. Its mission is to enable the production of various bio-based products, including pharmaceuticals, food additives, chemicals, and fuels, through metabolic engineering. The society hosts the Metabolic Engineering Conference biennially, offering researchers opportunities for knowledge exchange and collaboration.
2025.06.20 View 4940 -
KAIST Accelerates Synthetic Microbe Design by Discovering Novel Enzymes Using AI
< (From left) Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering (top), Hongkeun Ji, PhD candidate of the Department of Chemical and Biomolecular Engineering (top), Ha Rim Kim, PhD candidate of the Department of Chemical and Biomolecular Engineering, and Dr. Gi Bae Kim of the BioProcess Engineering Research Center >
Enzymes are proteins that catalyze biochemical reactions within cells and play a pivotal role in metabolic processes. Accordingly, identifying the functions of novel enzymes is a critical task in the construction of microbial cell factories.
A KAIST research team has leveraged artificial intelligence (AI) to design novel enzymes that do not exist in nature, significantly accelerating microbial cell factory development and boosting the potential for next-generation biotechnological applications such as drug development and biofuel production.
KAIST (represented by President Kwang-Hyung Lee) announced on the 21st of April that Distinguished Professor Sang Yup Lee and his team from the Department of Chemical and Biomolecular Engineering have published a review titled “Enzyme Functional Classification Using Artificial Intelligence,” which outlines the advancement of AI-based enzyme function prediction technologies and analyzes how AI has contributed to the discovery and design of new enzymes.
Professor Lee’s team systematically reviewed the development of enzyme function prediction technologies utilizing machine learning and deep learning, offering a comprehensive analysis.
From sequence similarity-based prediction methods to the integration of convolutional neural networks (CNNs), recurrent neural networks (RNNs), graph neural networks (GNNs), and transformer-based large language models, the paper covers a broad range of AI applications. It analyzes how these technologies extract meaningful information from protein sequences and enhance prediction accuracy.
In particular, enzyme function prediction using deep learning goes beyond simple sequence similarity analysis. By automatically extracting structural and evolutionary features embedded in amino acid sequences, deep learning enables more precise predictions of catalytic functions.
This highlights the unique advantages of AI models compared to traditional bioinformatics approaches.
Moreover, the review suggests that the advancement of generative AI will move future research beyond predicting existing functions to generating entirely new enzymes with functions not found in nature. This shift is expected to profoundly impact the trajectory of biotechnology and synthetic biology.
< Figure 1. Extraction of enzyme characteristics and function prediction using various deep learning structures >
Ha Rim Kim, a Ph.D. candidate and co-first author from the Department of Chemical and Biomolecular Engineering, stated, “AI-based enzyme function prediction and enzyme design are highly important across various fields including metabolic engineering, synthetic biology, and healthcare.”
Distinguished Professor Sang Yup Lee added, “AI-powered enzyme function prediction shows the potential to solve diverse biological problems and will significantly contribute to accelerating research across the entire field.”
The review was published on March 28 in Trends in Biotechnology, a leading biotechnology journal issued by Cell Press.
※ Title: Enzyme Functional Classification Using Artificial Intelligence
※DOI: https://doi.org/10.1016/j.tibtech.2025.03.003
※ Author Information: Ha Rim Kim (KAIST, Co-first author), Hongkeun Ji (KAIST, Co-first author), Gi Bae Kim (KAIST, Third author), Sang Yup Lee (KAIST, Corresponding author)
This research was supported by the Ministry of Science and ICT under the project Development of Core Technologies for Advanced Synthetic Biology to Lead the Bio-Manufacturing Industry (aimed at replacing petroleum-based chemicals), and also by joint support from the Ministry of Science and ICT and the Ministry of Health and Welfare for the project Development of Novel Antibiotic Structures Using Deep Learning-Based Synthetic Biology.
2025.04.07 View 8127 -
KAIST provides a comprehensive resource on microbial cell factories for sustainable chemical production
In silico analysis of five industrial microorganisms identifies optimal strains and metabolic engineering strategies for producing 235 valuable chemicals
Climate change and the depletion of fossil fuels have raised the global need for sustainable chemical production. In response to these environmental challenges, microbial cell factories are gaining attention as eco-friendly platforms for producing chemicals using renewable resources, while metabolic engineering technologies to enhance these cell factories are becoming crucial tools for maximizing production efficiency. However, difficulties in selecting suitable microbial strains and optimizing complex metabolic pathways continue to pose significant obstacles to practical industrial applications.
KAIST (President Kwang-Hyung Lee) announced on 27th of March that Distinguished Professor Sang Yup Lee’s research team in the Department of Chemical and Biomolecular Engineering comprehensively evaluated the production capabilities of various industrial microbial cell factories using in silico simulations and, based on these findings, identified the most suitable microbial strains for producing specific chemicals as well as optimal metabolic engineering strategies.
Previously, researchers attempted to determine the best strains and efficient metabolic engineering strategies among numerous microbial candidates through extensive biological experiments and meticulous verification processes. However, this approach required substantial time and costs. Recently, the introduction of genome-scale metabolic models (GEMs), which reconstruct the metabolic networks within an organism based on its entire genome information, has enabled systematic analysis of metabolic fluxes via computer simulations. This development offers a new way to overcome limitations of conventional experimental approaches, revolutionizing both strain selection and metabolic pathway design.
Accordingly, Professor Lee’s team at the Department of Chemical and Biomolecular Engineering, KAIST, evaluated the production capabilities of five representative industrial microorganisms—Escherichia coli, Saccharomyces cerevisiae, Bacillus subtilis, Corynebacterium glutamicum, and Pseudomonas putida—for 235 bio-based chemicals. Using GEMs, the researchers calculated both the maximum theoretical yields and the maximum achievable yields under industrial conditions for each chemical, thereby establishing criteria to identify the most suitable strains for each target compound.
< Figure 1. Outline of the strategy for improving microbial cell factories using a genome-scale metabolic model (GEM) >
The team specifically proposed strategies such as introducing heterologous enzyme reactions derived from other organisms and exchanging cofactors used by microbes to expand metabolic pathways. These strategies were shown to increase yields beyond the innate metabolic capacities of the microorganisms, resulting in higher production of industrially important chemicals such as mevalonic acid, propanol, fatty acids, and isoprenoids.
Moreover, by applying a computational approach to analyze metabolic fluxes in silico, the researchers suggested strategies for improving microbial strains to maximize the production of various chemicals. They quantitatively identified the relationships between specific enzyme reactions and target chemical production, as well as the relationships between enzymes and metabolites, determining which enzyme reactions should be up- or down-regulated. Through this, the team presented strategies not only to achieve high theoretical yields but also to maximize actual production capacities.
< Figure 2. Comparison of production routes and maximum yields of useful chemicals using representative industrial microorganisms >
Dr. Gi Bae Kim, the first author of this paper from the KAIST BioProcess Engineering Research Center, explained, “By introducing metabolic pathways derived from other organisms and exchanging cofactors, it is possible to design new microbial cell factories that surpass existing limitations. The strategies presented in this study will play a pivotal role in making microbial-based production processes more economical and efficient.” In addition, Distinguished Professor Sang Yup Lee noted, “This research serves as a key resource in the field of systems metabolic engineering, reducing difficulties in strain selection and pathway design, and enabling more efficient development of microbial cell factories. We expect it to greatly contribute to the future development of technologies for producing various eco-friendly chemicals, such as biofuels, bioplastics, and functional food materials.”
This research was conducted with the support from the Development of platform technologies of microbial cell factories for the next-generation biorefineries project and Development of advanced synthetic biology source technologies for leading the biomanufacturing industry project (Project Leader: Distinguished Professor Sang Yup Lee, KAIST) from National Research Foundation supported by the Korean Ministry of Science and ICT.
2025.03.27 View 8162 -
KAIST Develops Eco-Friendly, Nylon-Like Plastic Using Microorganisms
Poly(ester amide) amide is a next-generation material that combines the advantages of PET (polyester) and nylon (polyamide), two widely used plastics. However, it could only be produced from fossil fuels, which posed environmental concerns. Using microorganisms, KAIST researchers have successfully developed a new bio-based plastic to replace conventional plastic.
KAIST (represented by President Kwang Hyung Lee) announced on the 20th of March that a research team led by Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering has developed microbial strains through systems metabolic engineering to produce various eco-friendly, bio-based poly(ester amide)s. The team collaborated with researchers from the Korea Research Institute of Chemical Technology (KRICT, President Young-Kook Lee) to analyze and confirm the properties of the resulting plastic.
Professor Sang Yup Lee’s research team designed new metabolic pathways that do not naturally exist in microorganisms, and developed a platform microbial strain capable of producing nine different types of poly(ester amide)s, including poly(3-hydroxybutyrate-ran-3-aminopropionate) and poly(3-hydroxybutyrate-ran-4-aminobutyrate).
Using glucose derived from abundant biomass sources such as waste wood and weeds, the team successfully produced poly(ester amide)s in an eco-friendly manner. The researchers also confirmed the potential for industrial-scale production by demonstrating high production efficiency (54.57 g/L) using fed-batch fermentation of the engineered strain.
In collaboration with researchers Haemin Jeong and Jihoon Shin from KRICT, the KAIST team analyzed the properties of the bio-based plastic and found that it exhibited characteristics similar to high-density polyethylene (HDPE). This means the new plastic is not only eco-friendly but also strong and durable enough to replace conventional plastics.
The engineered strains and strategies developed in this study are expected to be useful not only for producing various poly(ester amide)s but also for constructing metabolic pathways for the biosynthesis of other types of polymers.
Professor Sang Yup Lee stated, “This study is the first to demonstrate the possibility of producing poly(ester amide)s (plastics) through a renewable bio-based chemical process rather than relying on the petroleum-based chemical industry. We plan to further enhance the production yield and efficiency through continued research.”
The study was published online on March 17 in the international journal Nature Chemical Biology.
·Title: Biosynthesis of poly(ester amide)s in engineered Escherichia coli
·DOI: 10.1038/s41589-025-01842-2
·Authors: A total of seven authors including Tong Un Chae (KAIST, first author), So Young Choi (KAIST, second author), Da-Hee Ahn (KAIST, third author), Woo Dae Jang (KAIST, fourth author), Haemin Jeong (KRICT, fifth author), Jihoon Shin (KRICT, sixth author), and Sang Yup Lee (KAIST, corresponding author).
This research was supported by the Ministry of Science and ICT (MSIT) under the Eco-Friendly Chemical Technology Development Project as part of the "Next-Generation Biorefinery Technology Development to Lead the Bio-Chemical Industry" initiative (project led by Distinguished Professor Sang Yup Lee at KAIST).
2025.03.24 View 10222 -
KAIST Researchers Suggest an Extraordinary Alternative to Petroleum-based PET - Bacteria!
< (From left) Dr. Cindy Pricilia, Ph.D. Candidate Cheon Woo Moon, Distinguished Professor Sang Yup Lee >
Currently, the world is suffering from environmental problems caused by plastic waste. The KAIST research team has succeeded in producing a microbial-based plastic that is biodegradable and can replace existing PET bottles, making it a hot topic.
Our university announced on the 7th of November that the research team of Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering has succeeded in developing a microbial strain that efficiently produces pseudoaromatic polyester monomer to replace polyethylene terephthalate (PET) using systems metabolic engineering.
Pseudoaromatic dicarboxylic acids have better physical properties and higher biodegradability than aromatic polyester (PET) when synthesized as polymers, and are attracting attention as an eco-friendly monomer* that can be synthesized into polymers. The production of pseudoaromatic dicarboxylic acids through chemical methods has the problems of low yield and selectivity, complex reaction conditions, and the generation of hazardous waste.
*Monomer: A material for making polymers, which is used to synthesize polymers by polymerizing monomers together
< Figure. Overview of pseudoaromatic dicarboxylic acid production using metabolically engineered C. glutamicum. >
To solve this problem, Professor Sang Yup Lee's research team used metabolic engineering to develop a microbial strain that efficiently produces five types of pseudoaromatic dicarboxylic acids, including 2-pyrone-4,6-dicarboxylic acid and four types of pyridine dicarboxylic acids (2,3-, 2,4-, 2,5-, 2,6-pyridine dicarboxylic acids), in Corynebacterium, a bacterium mainly used for amino acid production.
The research team used metabolic engineering techniques to build a platform microbial strain that enhances the metabolic flow of protocatechuic acid, which is used as a precursor for several pseudoaromatic dicarboxylic acids, and prevents the loss of precursors.
Based on this, the genetic manipulation target was discovered through transcriptome analysis, producing 76.17 g/L of 2-pyrone-4,6-dicarboxylic acid, and by newly discovering and constructing three types of pyridine dicarboxylic acid production metabolic pathways, successfully producing 2.79 g/L of 2,3-pyridine dicarboxylic acid, 0.49 g/L of 2,4-pyridine dicarboxylic acid, and 1.42 g/L of 2,5-pyridine dicarboxylic acid.
In addition, the research team confirmed the production of 15.01 g/L through the construction and reinforcement of the 2,6-pyridine dicarboxylic acid biosynthesis pathway, successfully producing a total of five similar aromatic dicarboxylic acids with high efficiency.
In conclusion, the team succeeded in producing 2,4-, 2,5-, and 2,6-pyridine dicarboxylic acids at the world's highest concentration. In particular, 2,4-, 2,5-pyridine dicarboxylic acid achieved production on the scale of g/L, which was previously produced in extremely small amounts (mg/L).
Based on this study, it is expected that it will be applied to various polyester production industrial processes, and it is also expected that it will be actively utilized in research on the production of similar aromatic polyesters.
Professor Sang Yup Lee, the corresponding author, said, “The significance lies in the fact that we have developed an eco-friendly technology that efficiently produces similar aromatic polyester monomers based on microorganisms,” and “This study will help the microorganism-based bio-monomer industry replace the petrochemical-based chemical industry in the future.”
The results of this study were published in the international academic journal, the Proceedings of the National Academy of Sciences of United States of America (PNAS) on October 30th.
※ Paper title: Metabolic engineering of Corynebacterium glutamicum for the production of pyrone and pyridine dicarboxylic acids
※ Author information: Jae Sung Cho (co-first author), Zi Wei Luo (co-first author), Cheon Woo Moon (co-first author), Cindy Prabowo (co-author), Sang Yup Lee (corresponding author) - a total of 5 people
This study was conducted with the support of the Development of Next-generation Biorefinery Platform Technologies for Leading Bio-based Chemicals Industry Project and the Development of Platform Technologies of Microbial Cell Factories for the Next-generation Biorefineries Project (Project leader: Professor Sang Yup Lee) from the National Research Foundation supported by the Ministry of Science and Technology and ICT of Korea.
2024.11.08 View 14722 -
KAIST finds ways for Bacteria to produce PET-like materials
Among various eco-friendly polymers, polyhydroxyalkanoates (PHA) stand out for their excellent biodegradability and biocompatibility. They decompose naturally in soil and marine environments and are used in applications such as food packaging and medical products. However, natural PHA produced to date has faced challenges meeting various physical property requirements, such as durability and thermal stability, and has been limited in its commercial application due to low production concentrations. In light of this, KAIST researchers have recently developed a technology that could play a crucial role in solving the environmental pollution problem caused by plastics.
KAIST (represented by President Kwang-Hyung Lee) announced on August 26th that a research team led by Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering, including Dr. Youngjoon Lee and master's student Minju Kang, has successfully developed a microbial strain that efficiently produces aromatic polyester* using systems metabolic engineering.
※ Aromatic polyester: A polymer containing aromatic compounds (specific carbon ring structures like benzene) and ester bonds.
In this study, the research team used metabolic engineering to enhance the metabolic flux of the biosynthetic pathway for the aromatic monomer phenyllactate (PhLA) in E. coli. They manipulated the metabolic pathway to increase the polymer fraction accumulated within the cells and employed computer simulations to predict the structure of PHA synthase and improve the enzyme based on the structure-function relationship.
Through subsequent fermentation optimization, the team achieved the world’s highest concentration (12.3±0.1 g/L) for the efficient production of poly (PhLA) and successfully produced polyester through a 30L scale fed-batch fermentation, demonstrating the possibility of industrial-level production. The produced aromatic polyesters showed enhanced thermal properties, improved mechanical properties, and potential for use as drug delivery carriers.
< Figure 1. Development schematics of aromatic polyester producing microorganisms >
The research team also demonstrated that an exogenous phasin protein* plays a crucial role in increasing the intracellular polymer accumulation fraction, which is directly related to the economic feasibility and efficiency of non-natural PHA production. They improved PHA synthase using a rational enzyme design approach, predicting the three-dimensional structure of the enzyme through homology modeling (a method of predicting the three-dimensional structure of a new protein based on the structure of similar proteins) followed by molecular docking simulations (simulations that predict how well a monomer can bind to an enzyme) and molecular dynamics simulations (simulations that predict how molecules move and interact over time) to upgrade the enzyme into a mutant enzyme with enhanced monomer polymerization efficiency.
※ Exogenous phasin protein: Phasin is a protein related to PHA production, interacting with the cytoplasmic environment on the surface of granules of PHA, and playing a role in polymer accumulation and controlling the number and size of granules. In this study, genes encoding phasin proteins derived from various natural PHA-producing microorganisms were selected and introduced.
Dr. Youngjoon Lee, co-first author of the paper, explained, "The significance of this study lies in the fact that we have achieved the world's highest concentration of microbial-based aromatic polyester production using eco-friendly materials and methods. This technology is expected to play a crucial role in addressing the environmental pollution caused by plastics." Distinguished Professor Sang Yup Lee added, "This study, which presents various strategies for the high-efficiency production of useful polymers via systems metabolic engineering, is expected to make a significant contribution to solving climate change issues, particularly the recent plastic problem."
< Figure 2. Detailed development strategy for aromatic polyester producing microorganisms >
The research findings were published on August 21st in Trends in Biotechnology, published by Cell, an international academic journal.
※ Paper Title: “Microbial production of an aromatic homopolyester”
※ Author Information: Youngjoon Lee (KAIST, co-first author), Minju Kang (KAIST, co-first author), Woo Dae Jang (KAIST, second author), So Young Choi (KAIST, third author), Jung Eun Yang (KAIST, fourth author), Sang Yup Lee (KAIST, corresponding author), totaling six authors.
This research was supported by the "Development of Next-Generation Biorefinery Platform Technologies for Leading the Bio-based Chemicals Industry" project led by Distinguished Professor Sang Yup Lee at KAIST, under the eco-friendly chemical technology development project aimed at substituting petroleum, funded by the Ministry of Science and ICT. It was also supported by the "Development of Platform Technology for the Production of Novel Aromatic Bioplastic Using Microbial Cell Factories" project (Project Leader: Si Jae Park, Ewha Woman’s University).
2024.08.28 View 11156 -
KAIST Develops Microbial Liquid Egg Substitute
A team of researchers published a paper on developing a substitute for eggs using microorganisms, grabbing international attention. It is expected that the development of egg substitutes using non-animal raw materials will solve the problems of factory farming, which causes problems like increased emission of greenhouse gas and waste, and contribute to building a sustainable food system that allows easy protein intake.
KAIST (President Kwang-Hyung Lee) announced that Research Professor Kyeong Rok Choi from the Biological Process Research Center and Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering have published a paper on the development of an "Eco-Friendly Liquid Egg Substitute Derived from Microorganisms."
Eggs play a crucial role in various culinary applications due to their unique physicochemical properties such as gelling, foaming, and emulsifying, while also providing essential nutrients. However, traditional egg production is not only unethical and resource-intensive but also has significant environmental impacts such as greenhouse gas emissions and waste issues. Additionally, factors such as wars and trade regulations have led to significant increases in egg prices, highlighting food security concerns. In response to these issues, there has been growing interest in egg substitutes made from non-animal sources to establish a sustainable food system.
Although there has been progress in developing non-animal protein-based egg substitutes, no substitute has been able to fully replicate the essential functional properties of liquid eggs, such as gelling and foaming, while also providing complete nutrition. In this context, the research team aimed to develop a liquid egg substitute using microbial biomass, which has a protein content comparable to that of meat per unit dry mass. Various microorganisms, such as yeast, Bacillus, lactic acid bacteria, and other probiotics, have been proven safe through long-term human consumption. Microbial biomass requires fewer resources like water and land during production, and possesses high-quality nutrients, making it a promising sustainable food resource.
< Figure 1. Comparison of heat treatment results of microbial pellets and microbial lysates >
However, the semi-solid microbial biomass recovered through microbial cultivation was observed to turn liquid upon heating, unlike liquid egg. To address this, the research team devised a microbial lysate by breaking down the cell walls and cell membranes of microorganisms, which correspond to the eggshell. They found that the microbial lysate's proteins coagulated when heated and formed a gel similar to that of liquid egg. The gel formed from the heated microbial lysate was found to have microscopic structures and physical properties similar to those of boiled eggs. The addition of microbial-derived edible enzymes or plant-based materials allowed for the adjustment of its properties, enabling the creation of various textures.
Furthermore, the researchers demonstrated that the microbial lysate could form stable foams widely used in baking, such as meringues (made from egg whites). They successfully baked meringue cookies using this lysate, showing its potential as a functional liquid egg substitute.
Distinguished Professor Sang Yup Lee stated, "This substitute has excellent nutritional components, making it suitable for regular food consumption. It is especially promising as emergency food for long-term space travel, wartime situations, and other emergencies. More importantly, it contributes to securing a sustainable food system."
< Figure 2. Example of foaming ability of microbial lysate and meringue cookie production >
< Figure 3. Example of foaming ability of microbial lysate and meringue cookie production >
The paper was published online in the journal npj Science of Food, issued by Nature.
- Paper Title: Microbial lysates repurposed as liquid egg substitutes
- Authors: Kyeong Rok Choi (first author), Da-Hee Ahn, Seok Yeong Jung, YuHyun Lee, and Sang Yup Lee (corresponding author)
This research was supported by the Ministry of Science and ICT's project for developing eco-friendly chemical technologies to replace petroleum (Project Leader: Distinguished Professor Sang Yup Lee, KAIST) and the Rural Development Administration's Agricultural Microorganisms Project Group (Director: Professor Pan-sik Jang, Seoul National University) for developing protein production technology from inorganic substances through microbial metabolic system control (Project Leader: Research Professor Kyeong Rok Choi, KAIST).
2024.07.05 View 10440 -
KAIST introduces microbial food as a strategy food production of the future
The global food crisis is increasing due to rapid population growth and declining food productivity to climate change. Moreover, today's food production and supply system emit a huge amount of carbon dioxide, reaching 30% of the total amount emitted by humanity, aggravating climate change. Sustainable and nutritious microbial food is attracting attention as a key to overcoming this impasse.
KAIST (President Kwang Hyung Lee) announced on April 12th that Research Professor Kyeong Rok Choi of the BioProcess Engineering Research Center and Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering published a paper that proposes a direction of research on ‘microbial food production from sustainable raw materials.’
Microbial food refers to various foods and food ingredients produced using microorganisms. Microbial biomass contains a large amount of protein per unit in dry mass, comparable to that of meat, and emits the smallest amount of carbon dioxide and is required to produce a unit mass compared to various livestock, fish, shellfish, and crops. Since the amount of water and space requirement is small, it can be an eco-friendly, sustainable and highly nutritious food resource.
Fermented foods are the most readily available microbial foods around us. Although the proportion of microbial biomass in fermented foods is small, compounds with relatively low nutritional value, such as carbohydrates, are consumed during the fermentation process, and as microorganisms proliferate, the content of nutrients with higher nutritional value, such as proteins and vitamins, increases.
Various food compounds isolated and purified from biomass or culture media obtained through microbial culture are also a branch of microbial food. Examples that can be found around us include various amino acids, including monosodium glutamate, food proteins, enzymes, flavoring compounds, food colorings, and bioactive substances.
< Figure 1. Schematic diagram portraying various microbial biomass production strategies utlizing sustainable feedstocks >
Lastly, the most ultimate and fundamental form of microbial food can be said to be microbial biomass or extracts produced through microbial culture and foods cooked using them. A representative example is single-cell protein, which collectively refers to microbial biomass or microbial proteins extracted from it.
In this paper, the researchers comprehensively covered various non-edible raw materials and strategies for using them that can be used to produce microbial food in a more sustainable way. Furthermore, it covers various microbial foods that are actually produced in the industry using the relevant raw materials and their characteristics, as well as prospects for the production and generalization of sustainable microbial foods.
Research Professor Kyeong Rok Choi, the first author of this paper, said, “Microbial foods produced from various sustainable raw materials will soon be commonly encountered at our tables.” Second author Seok Yeong Jung, a doctoral student, also said, “Microbial foods of the future will not be limited foods consumed only out of a sense of obligation to the environment, but will be complete foods that are consumed by choice because of their nutritional value and taste.” In addition, Distinguished Professor Sang Yup Lee said, “It is time for the industry and academia, as well as the public and private sectors, to cooperate more closely so that more diverse microbial foods can be developed and supplied in order to create a sustainable society for ourselves and our descendants.”
< Figure 2. Compositions and environmental footprints of animal, plant and microbial biomass. >
This paper was published online on April 9 in ‘Nature Microbiology’ published by Nature.
※ Paper title: From sustainable feedstocks to microbial foods
※ Author information: Kyeong Rok Choi (first author), Seok Yeong Jung (second author) and Sang Yup Lee (corresponding author)
This research was conducted under the development of platform technologies of microbial cell factories for the next-generation biorefineries project (project leader KAIST Distinguished Professor Sang Yup Lee) supported by the Ministry of Science and ICT and the Cooperative Research Program for Agriculture Science and Technology Development (Project leader KAIST Research Professor Kyeong Rok Choi) of the Agricultural Microbiology Project Group (Director, Professor Pahn-Shick Chang) supported by the Rural Development Administration.
2024.04.12 View 11733