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Genomic and transcriptomic landscape of <i>Escherichia coli</i> BL21(DE3)
Kim, Sinyeon,Jeong, Haeyoung,Kim, Eun-Youn,Kim, Jihyun F.,Lee, Sang Yup,Yoon, Sung Ho Oxford University Press 2017 Nucleic acids research Vol.45 No.9
<P><B>Abstract</B></P><P><I>Escherichia coli</I> BL21(DE3) has long served as a model organism for scientific research, as well as a workhorse for biotechnology. Here we present the most current genome annotation of <I>E. coli</I> BL21(DE3) based on the transcriptome structure of the strain that was determined for the first time. The genome was annotated using multiple automated pipelines and compared to the current genome annotation of the closely related strain, <I>E. coli</I> K-12. High-resolution tiling array data of <I>E. coli</I> BL21(DE3) from several different stages of cell growth in rich and minimal media were analyzed to characterize the transcriptome structure and to provide supporting evidence for open reading frames. This new integrated analysis of the genomic and transcriptomic structure of <I>E. coli</I> BL21(DE3) has led to the correction of translation initiation sites for 88 coding DNA sequences and provided updated information for most genes. Additionally, 37 putative genes and 66 putative non-coding RNAs were also identified. The panoramic landscape of the genome and transcriptome of <I>E. coli</I> BL21(DE3) revealed here will allow us to better understand the fundamental biology of the strain and also advance biotechnological applications in industry.</P>
Overexpression of YbeD in Escherichia coli Enhances Thermotolerance
( Sinyeon Kim ),( Youngshin Kim ),( Sung Ho Yoon ) 한국미생물생명공학회(구 한국산업미생물학회) 2019 Journal of microbiology and biotechnology Vol.29 No.3
Heat-resistant microbial hosts are required for bioprocess development using high cell density cultivations at the industrial scale. We report that the thermotolerance of Escherichia coli can be enhanced by overexpressing ybeD, which was known to encode a hypothetical protein of unknown function. In the wild-type E. coli BL21(DE3), ybeD transcription level increased over five-fold when temperature was increased from 37°C to either 42°C or 46°C. To study the function of ybeD, a deletion strain and an overexpression strain were constructed. At 46°C, in comparison to the wild type, the ybeD-deletion reduced cell growth half-fold, and the ybeD-overexpression promoted cell growth over two-fold. The growth enhancement by ybeD-overexpression was much more pronounced at 46°C than 37°C. The ybeD-overexpression was also effective in other E. coli strains of MG1655, W3110, DH10B, and BW25113. These findings reveal that ybeD gene plays an important role in enduring high-temperature stress, and that ybeD-overexpression can be a prospective strategy to develop thermotolerant microbial hosts.
( Haeyoung Jeong ),( Seung-won Lee ),( Sun Hong Kim ),( Eun-youn Kim ),( Sinyeon Kim ),( Sung Ho Yoon ) 한국미생물생명공학회(구 한국산업미생물학회) 2017 Journal of microbiology and biotechnology Vol.27 No.6
Butanol is a promising alternative to ethanol and is desirable for use in transportation fuels and additives to gasoline and diesel fuels. Microbial production of butanol is challenging primarily because of its toxicity and low titer of production. Herein, we compared the transcriptome and phenome of wild-type Escherichia coli and its butanol-tolerant evolved strain to understand the global cellular physiology and metabolism responsible for butanol tolerance. When the ancestral butanol-sensitive E. coli was exposed to butanol, gene activities involved in respiratory mechanisms and oxidative stress were highly perturbed. Intriguingly, the evolved butanol-tolerant strain behaved similarly in both the absence and presence of butanol. Among the mutations occurring in the evolved strain, cis-regulatory mutations may be the cause of butanol tolerance. This study provides a foundation for the rational design of the metabolic and regulatory pathways for enhanced biofuel production.
Salmonella typhimurium with γ-radiation induced H2AX phosphorylation and apoptosis in melanoma.
Yoon, Won Suck,Kim, Sinyeon,Seo, Sungchul,Park, Yongkeun Japan Society for Bioscience, Biotechnology, and A 2014 Bioscience, Biotechnology, and Biochemistry Vol.78 No.6
<P>To investigate the combinatorial effects using Salmonella and γ-radiation, the Salmonella typhimurium infection in combination with γ-radiation was investigated on melanoma. We showed that ROS expression and H2AX phosphorylation increased during stress by γ-radiation irrespective of Salmonella infection, inducing apoptosis by caspase-3 and bcl2 in tumor cells. In addition, tumor growth was suppressed by this combinatory therapy suggesting candidates for radiation therapy against melanoma.</P>