• Journal of Microbiology and Biotechnology
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• 제32권8호
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• pp.1026-1033
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• 2022

This study presents a novel DNA part characterization technique that increases throughput by combinatorial DNA part assembly, solid plate-based quantitative fluorescence assay for phenotyping, and barcode tagging-based long-read sequencing for genotyping. We confirmed that the fluorescence intensities of colonies on plates were comparable to fluorescence at the single-cell level from a high-end, flow-cytometry device and developed a high-throughput image analysis pipeline. The barcode tagging-based long-read sequencing technique enabled rapid identification of all DNA parts and their combinations with a single sequencing experiment. Using our techniques, forty-four DNA parts (21 promoters and 23 RBSs) were successfully characterized in 72 h without any automated equipment. We anticipate that this high-throughput and easy-to-use part characterization technique will contribute to increasing part diversity and be useful for building genetic circuits and metabolic pathways in synthetic biology.

• Journal of Ginseng Research
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• 제48권2호
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• pp.140-148
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• 2024

Synthetic biology approaches offer potential for large-scale and sustainable production of natural products with bioactive potency, including ginsenosides, providing a means to produce novel compounds with enhanced therapeutic properties. Ginseng, known for its non-toxic and potent qualities in traditional medicine, has been used for various medical needs. Ginseng has shown promise for its antioxidant and neuroprotective properties, and it has been used as a potential agent to boost immunity against various infections when used together with other drugs and vaccines. Given the increasing demand for ginsenosides and the challenges associated with traditional extraction methods, synthetic biology holds promise in the development of therapeutics. In this review, we discuss recent developments in microorganism producer engineering and ginsenoside production in microorganisms using synthetic biology approaches.

• Journal of Microbiology and Biotechnology
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• 제33권4호
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• pp.552-558
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• 2023

Levulinic acid (LA) is a valuable chemical used in fuel additives, fragrances, and polymers. In this study, we proposed possible biosynthetic pathways for LA production from lignin and poly(ethylene terephthalate). We also created a genetically encoded biosensor responsive to LA, which can be used for screening and evolving the LA biosynthesis pathway genes, by employing an LvaR transcriptional regulator of Pseudomonas putida KT2440 to express a fluorescent reporter gene. The LvaR regulator senses LA as a cognate ligand. The LA biosensor was first examined in an Escherichia coli strain and was found to be non-functional. When the host of the LA biosensor was switched from E. coli to P. putida KT2440, the LA biosensor showed a linear correlation between fluorescence intensity and LA concentration in the range of 0.156-10 mM LA. In addition, we determined that 0.156 mM LA was the limit of LA detection in P. putida KT2440 harboring an LA-responsive biosensor. The maximal fluorescence increase was 12.3-fold in the presence of 10 mM LA compared to that in the absence of LA. The individual cell responses to LA concentrations reflected the population-averaged responses, which enabled high-throughput screening of enzymes and metabolic pathways involved in LA biosynthesis and sustainable production of LA in engineered microbes.

• 과학기술학연구
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• 제16권2호
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• pp.33-63
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• 2016

이 논문은 포스트 게놈 시대에 합성생물학 연구자들과 트랜스휴머니스트들의 자연관과 진화개념을 비교분석하는 것을 목적으로 하고 있다. 2000년대 새롭게 등장한 합성생물학은 "합리적 설계"와 "방향적 진화"라는 두 가지 핵심적인 개념을 통해 생명 시스템을 디자인하는 것을 가능케 했다. 인간이 생명체를 설계해 만들어내고 진화과정을 가속화시킬 뿐만 아니라 특정 방향으로 유도한다는 점에서, 자연적인 것과 인공적인 것 사이의 경계가 무너지는 것 아닌가 하는 우려가 제기되었다. 이렇게 합성생물학으로 재구성된 자연을 어떻게 받아들여야 할 것인가? 진화의 속도와 방향에 영향을 주는 연구를 어떻게 정당화할 수 있는가? 합성생물학과 트랜스휴머니즘은 어떤 지적 자산을 공유하고 있나? 과학기술의 상업화와 같은 사회경제적 요소가 분야의 흐름에 영향을 주지는 않은지? 자연의 도덕적 권위는 사라졌는가? 본 논문은 합성생물학을 선도하고 있는 세 명의 과학자와 최근 대표적 트랜스휴머니스트로 떠오르고 있는 옥스퍼드 대학의 철학자들을 관점을 소개하고 비교분석하여 이 질문들에 답하려고 한다.

• Journal of Microbiology and Biotechnology
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• 제32권11호
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• pp.1373-1381
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• 2022

Fructan is a polysaccharide composed of fructose and can be classified into several types, such as inulin, levan, and fructo-oligosaccharides, based on their linkage patterns and degree of polymerization. Owing to its structural and functional diversity, fructan has been used in various fields including prebiotics, foods and beverages, cosmetics, and pharmaceutical applications. With increasing interest in fructans, efficient and straightforward production methods have been explored. Since the 1990s, yeast cells have been employed as producers of recombinant enzymes for enzymatic conversion of fructans including fructosyltransferases derived from various microbes and plants. More recently, yeast cell factories are highlighted as efficient workhorses for fructan production by direct fermentation. In this review, recent advances and strategies for fructan biosynthesis by yeast cell factories are discussed.

• Journal of Microbiology and Biotechnology
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• 제33권11호
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• pp.1513-1520
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• 2023

Kex2 protease (Kex2p) is a membrane-bound serine protease responsible for the proteolytic maturation of various secretory proteins by cleaving after dibasic residues in the late Golgi network. In this study, we present an application of Kex2p as an alternative endoprotease for the in vitro processing of recombinant fusion proteins produced by the yeast Saccharomyces cerevisiae. The proteins were expressed with a fusion partner connected by a Kex2p cleavage sequence for enhanced expression and easy purification. To avoid in vivo processing of fusion proteins by Kex2p during secretion and to guarantee efficient removal of the fusion partners by in vitro Kex2p processing, P₁', P₂', P₄, and P₃ sites of Kex2p cleavage sites were elaborately manipulated. The general use of Kex2p in recombinant protein production was confirmed using several recombinant proteins.

• Journal of Microbiology and Biotechnology
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• 제29권6호
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• pp.845-855
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• 2019

Synthetic biology builds programmed biological systems for a wide range of purposes such as improving human health, remedying the environment, and boosting the production of valuable chemical substances. In recent years, the rapid development of synthetic biology has enabled synthetic bacterium-based diagnoses and therapeutics superior to traditional methodologies by engaging bacterial sensing of and response to environmental signals inherent in these complex biological systems. Biosynthetic systems have opened a new avenue of disease diagnosis and treatment. In this review, we introduce designed synthetic bacterial systems acting as living therapeutics in the diagnosis and treatment of several diseases. We also discuss the safety and robustness of genetically modified synthetic bacteria inside the human body.

• Genomics & Informatics
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• 제11권2호
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• pp.76-82
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• 2013

Over the past decade or so, dramatic developments in our ability to experimentally determine the content and function of genomes have taken place. In particular, next-generation sequencing technologies are now inspiring a new understanding of bacterial transcriptomes on a global scale. In bacterial cells, whole-transcriptome studies have not received attention, owing to the general view that bacterial genomes are simple. However, several recent RNA sequencing results are revealing unexpected levels of complexity in bacterial transcriptomes, indicating that the transcribed regions of genomes are much larger and complex than previously anticipated. In particular, these data show a wide array of small RNAs, antisense RNAs, and alternative transcripts. Here, we review how current transcriptomics are now revolutionizing our understanding of the complexity and regulation of bacterial transcriptomes.

• Journal of Microbiology and Biotechnology
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• 제29권5호
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• pp.667-686
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• 2019

Streptomyces are attractive microbial cell factories that have industrial capability to produce a wide array of bioactive secondary metabolites. However, the genetic potential of the Streptomyces species has not been fully utilized because most of their secondary metabolite biosynthetic gene clusters (SM-BGCs) are silent under laboratory culture conditions. In an effort to activate SM-BGCs encoded in Streptomyces genomes, synthetic biology has emerged as a robust strategy to understand, design, and engineer the biosynthetic capability of Streptomyces secondary metabolites. In this regard, diverse synthetic biology tools have been developed for Streptomyces species with technical advances in DNA synthesis, sequencing, and editing. Here, we review recent progress in the development of synthetic biology tools for the production of novel secondary metabolites in Streptomyces, including genomic elements and genome engineering tools for Streptomyces, the heterologous gene expression strategy of designed biosynthetic gene clusters in the Streptomyces chassis strain, and future directions to expand diversity of novel secondary metabolites.