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Phage resistant Escherichia coli strains developed to reduce fermentation failure
A genome engineering-based systematic strategy for developing phage resistant Escherichia coli strains has been successfully developed through the collaborative efforts of a team led by Professor Sang Yup Lee, Professor Shi Chen, and Professor Lianrong Wang. This study by Xuan Zou et al. was published in Nature Communications in August 2022 and featured in Nature Communications Editors’ Highlights. The collaboration by the School of Pharmaceutical Sciences at Wuhan University, the First Affiliated Hospital of Shenzhen University, and the KAIST Department of Chemical and Biomolecular Engineering has made an important advance in the metabolic engineering and fermentation industry as it solves a big problem of phage infection causing fermentation failure. Systems metabolic engineering is a highly interdisciplinary field that has made the development of microbial cell factories to produce various bioproducts including chemicals, fuels, and materials possible in a sustainable and environmentally friendly way, mitigating the impact of worldwide resource depletion and climate change. Escherichia coli is one of the most important chassis microbial strains, given its wide applications in the bio-based production of a diverse range of chemicals and materials. With the development of tools and strategies for systems metabolic engineering using E. coli, a highly optimized and well-characterized cell factory will play a crucial role in converting cheap and readily available raw materials into products of great economic and industrial value. However, the consistent problem of phage contamination in fermentation imposes a devastating impact on host cells and threatens the productivity of bacterial bioprocesses in biotechnology facilities, which can lead to widespread fermentation failure and immeasurable economic loss. Host-controlled defense systems can be developed into effective genetic engineering solutions to address bacteriophage contamination in industrial-scale fermentation; however, most of the resistance mechanisms only narrowly restrict phages and their effect on phage contamination will be limited. There have been attempts to develop diverse abilities/systems for environmental adaptation or antiviral defense. The team’s collaborative efforts developed a new type II single-stranded DNA phosphorothioation (Ssp) defense system derived from E. coli 3234/A, which can be used in multiple industrial E. coli strains (e.g., E. coli K-12, B and W) to provide broad protection against various types of dsDNA coliphages. Furthermore, they developed a systematic genome engineering strategy involving the simultaneous genomic integration of the Ssp defense module and mutations in components that are essential to the phage life cycle. This strategy can be used to transform E. coli hosts that are highly susceptible to phage attack into strains with powerful restriction effects on the tested bacteriophages. This endows hosts with strong resistance against a wide spectrum of phage infections without affecting bacterial growth and normal physiological function. More importantly, the resulting engineered phage-resistant strains maintained the capabilities of producing the desired chemicals and recombinant proteins even under high levels of phage cocktail challenge, which provides crucial protection against phage attacks. This is a major step forward, as it provides a systematic solution for engineering phage-resistant bacterial strains, especially industrial bioproduction strains, to protect cells from a wide range of bacteriophages. Considering the functionality of this engineering strategy with diverse E. coli strains, the strategy reported in this study can be widely extended to other bacterial species and industrial applications, which will be of great interest to researchers in academia and industry alike. Fig. A schematic model of the systematic strategy for engineering phage-sensitive industrial E. coli strains into strains with broad antiphage activities. Through the simultaneous genomic integration of a DNA phosphorothioation-based Ssp defense module and mutations of components essential for the phage life cycle, the engineered E. coli strains show strong resistance against diverse phages tested and maintain the capabilities of producing example recombinant proteins, even under high levels of phage cocktail challenge.
Five Projects Ranked in the Top 100 for National R&D Excellence
Five KAIST research projects were selected as the 2021 Top 100 for National R&D Excellence by the Ministry of Science and ICT and the Korea Institute of Science & Technology Evaluation and Planning. The five projects are:-The development of E. coli that proliferates with only formic acid and carbon dioxide by Distinguished Professor Sang Yup Lee from the Department of Chemical and Biomolecular Engineering -An original reverse aging technology that restores an old human skin cell into a younger one by Professor Kwang-Hyun Cho from the Department of Bio and Brain Engineering-The development of next-generation high-efficiency perovskite-silicon tandem solar cells by Professor Byungha Shin from the Department of Materials Science and Engineering-Research on the effects of ultrafine dust in the atmosphere has on energy consumption by Professor Jiyong Eom from the School of Business and Technology Management-Research on a molecular trigger that controls the phase transformation of bio materials by Professor Myungchul Kim from the Department of Bio and Brain Engineering Started in 2006, an Evaluation Committee composed of experts in industries, universities, and research institutes has made the preliminary selections of the most outstanding research projects based on their significance as a scientific and technological development and their socioeconomic effects. The finalists went through an open public evaluation. The final 100 studies are from six fields: 18 from mechanics & materials, 26 from biology & marine sciences, 19 from ICT & electronics, 10 from interdisciplinary research, and nine from natural science and infrastructure. The selected 100 studies will receive a certificate and an award plaque from the minister of MSIT as well as additional points for business and institutional evaluations according to appropriate regulations, and the selected researchers will be strongly recommended as candidates for national meritorious awards. In particular, to help the 100 selected research projects become more accessible for the general public, their main contents will be provided in a free e-book ‘The Top 100 for National R&D Excellence of 2021’ that will be available from online booksellers.
Nanowerk Spotlight: Bacteria as environmentally friendly nanoparticle factories, Sep. 24, 2010
The Nanowerk.com is a leading portal site for nanotechnology and nanosciences, which runs a daily news section called “Spotlight.” On September 24, 2010, the Spotlight published an article on the latest developments of the research by a KAIST team headed by Distinguished Professor Sang-Yup Lee of the Chemical and Bimolecular Engineering Department. For the article, please click the link below: Nanowerk Spotlight: Bacteria as environmentally friendly nanoparticle factories, Sep. 24, 2010 By Michael Berger. http://www.nanowerk.com/spotlight/spotid=18188.php
Prof. Lee"s Team Pioneers Biotechnological Production of Chemical Using Renewable Materials
A research team led by Prof. Sang-Yup Lee of the Bio and Brain Engineering Department at KAIST has succeeded in engineering the bacterium E. coli to produce the industrial chemical putrescine, university authorities said on Monday (Aug. 31). Putrescine, a four carbon chain diamine, is an important platform chemical with a wide range of applications for the pharmaceutical, agrochemical and chemical industries. It is currently used to synthesize nylon-4,6, a widely used engineering plastic. The research result, published in the Biotechnology and Bioengineering journal, proviDrdes a renewable alternative to the traditional process using fossil fuels. Currently the production of putrescine on an industrial scale relies on chemical synthesis, which requires non-renewable petrochemicals and expensive catalyst systems. This process is highly toxic and flammable with potentially severe repercussions for both the environment and human health. "For the first time we have developed a metabolically engineered E. coli strain that efficiently produces putrescine," said Professor Lee. "The development of a bio-refinery for chemicals and materials is very important in a world where dependency on fossil fuels is an increasing concern." The team developed a strain of E.coli capable of producing putrescine through metabolic engineering. This is where a cell"s metabolic and regulatory networks are enhanced in order to increase production of a needed material. First the team weakened or deleted competing metabolic pathways within the E. coli strain before deleting pathways which cause putrescine degradation. They also amplified the crucial enzyme Spec C, which converts the chemical ornithine into putrescine. Finally the putrescine exporter, which allows excretion of intracellularly made putrescine, was engineered while a global regulator was engineered to further increase the concentration of putrescine. The final result of this process was an engineered E.coli strain which produced 24.2 g of putrescine per litre. However, as it was believed that putrescine is toxic to microorganisms the team had to study putrescine tolerance in E.coli before it could be engineered to overproduce the chemical to the levels needed for industrial production. The results revealed that E. coli can tolerate at least 0.5 M of putrescine, which is tenfold higher than the usual concentration in the cell. This level of tolerance was an important surprise as it means that E. coli can be engineered to overproduce putrescine to industrially competitive levels. "The previously expected toxicity of putrescine may explain why its microbial production has been overlooked," said Lee. "Now a metabolically engineered E. coli strain has been developed which is capable of efficiently producing putrescine using renewable methods to an industrial level. This metabolic engineering framework should be useful for developing metabolically engineered microorganisms for the efficient production of other chemicals from renewable resources," he added.
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