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Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs
Na, Dokyun,Yoo, Seung Min,Chung, Hannah,Park, Hyegwon,Park, Jin Hwan,Lee, Sang Yup Nature Publishing Group, a division of Macmillan P 2013 Nature biotechnology Vol.31 No.2
Small regulatory RNAs (sRNAs) regulate gene expression in bacteria. We designed synthetic sRNAs to identify and modulate the expression of target genes for metabolic engineering in Escherichia coli. Using synthetic sRNAs for the combinatorial knockdown of four candidate genes in 14 different strains, we isolated an engineered E. coli strain (tyrR- and csrA-repressed S17-1) capable of producing 2 g per liter of tyrosine. Using a library of 130 synthetic sRNAs, we also identified chromosomal gene targets that enabled substantial increases in cadaverine production. Repression of murE led to a 55% increase in cadaverine production compared to the reported engineered strain (XQ56 harboring the plasmid p15CadA). The design principles and the engineering strategy using synthetic sRNAs reported here are generalizable to other bacteria and applicable in developing superior producer strains. The ability to fine-tune target genes with designed sRNAs provides substantial advantages over gene-knockout strategies and other large-scale target identification strategies owing to its easy implementation, ability to modulate chromosomal gene expression without modifying those genes and because it does not require construction of strain libraries.
나도균(Dokyun Na),이필현(PhiHyoun Lee),이서우(Sean Lee),이도헌(Doheon Lee),이광형(Kwanghyung Lee),배명남(MyungNam Bae) 한국정보과학회 2003 한국정보과학회 학술발표논문집 Vol.30 No.2Ⅱ
다양한 바이오 정보 데이터베이스와 분석 도구들을 효율적으로 검색하고, 개별 데이터베이스에서는 얻을 수 없는 새로운 지식을 생성하기 위해서는 통합된 형태의 정보 검색 시스템이 필수적으로 요청된다. 여기서 우리는 바이오 정보 시스템 통합을 어렵게 하는 요소들을 살펴보고, 다중 질의 수행과 확장성 등을 기준으로, 현재 서비스되고 있는 바이오 정보 통합 시스템들의 특성을 분석 비교하였다. 또한 이를 기반으로 바이오 정보 통합 시스템의 구조를 제시하였다.
Ren, Jun,Na, Dokyun,Yoo, Seung Min Elsevier 2018 Journal of biotechnology Vol.288 No.-
<P><B>Abstract</B></P> <P>Bacterial transformation is a fundamental technology to deliver engineered plasmids into bacterial cells, which is essential in industrial protein production, chemical production, <I>etc</I>. Previously, we developed a simple chemico-physical transformation method that can be applied to various bacterial species. Here, to accelerate the advance of bacteria biotechnology we optimize our method by combinatorially evaluating chemical compounds (rubidium chloride, lithium acetate, cesium chloride, dimethyl sulfoxide, and magnesium chloride) for increasing membrane permeability and nanomaterials (sepiolite, gold(III) chloride, multiwalled carbon nanotube, and chitosan) for piercing the membranes. The best transformation efficiencies were achieved as follows; 2.84 × 10<SUP>4</SUP> CFU/μg DNA in <I>Lactococcus lactis</I> subsp. <I>lactics</I> (0.1 M CsCl and gold(III) chloride), 3.60 × 10<SUP>4</SUP> CFU/μg DNA in <I>Enterococcus faecalis</I> (1 M Li-acetate and MWCNT), 2.41 × 10<SUP>4</SUP> CFU/μg DNA in <I>Bacillus</I> sp. (0.01 M RbCl and sepiolite), 3.49 × 10<SUP>4</SUP> CFU/μg DNA (0.1 M RbCl and gold(III) chloride) in <I>Ralstonia eutropha</I> (also known as <I>Cupriavidus necator</I>) and 8.78 × 10<SUP>4</SUP> CFU/μg DNA (1 M RbCl and chitosan) in <I>Methylomonas</I> sp. DH-1. The efficiencies are up to 100-fold higher than those without optimization. Accordingly, our fast and simple chemico-physical transformation with chemical–nanomaterial optimization allows for the efficient DNA entry into various bacterial cells with high efficiency.</P> <P><B>Highlights</B></P> <P> <UL> <LI> A chemico-physical transformation method with high efficiency was developed. </LI> <LI> RbCl, LiAc, CsCl, DMSO, and MgCl2 were used for increasing membrane permeability. </LI> <LI> Sepiolite, gold(III) chloride, MWCNT, and chitosan were used for piercing the membranes. </LI> <LI> High efficiency was achieved by optimizing chemical–nanomaterial combinations. </LI> <LI> The efficiencies are up to 100-fold higher than those without optimization. </LI> </UL> </P>