http://chineseinput.net/에서 pinyin(병음)방식으로 중국어를 변환할 수 있습니다.
변환된 중국어를 복사하여 사용하시면 됩니다.
The architecture of ArgR-DNA complexes at the genome-scale in <i>Escherichia coli</i>
Cho, Suhyung,Cho, Yoo-Bok,Kang, Taek Jin,Kim, Sun Chang,Palsson, Bernhard,Cho, Byung-Kwan Oxford University Press 2015 Nucleic acids research Vol.43 No.6
<P>DNA-binding motifs that are recognized by transcription factors (TFs) have been well studied; however, challenges remain in determining the <I>in vivo</I> architecture of TF-DNA complexes on a genome-scale. Here, we determined the <I>in vivo</I> architecture of <I>Escherichia coli</I> arginine repressor (ArgR)-DNA complexes using high-throughput sequencing of exonuclease-treated chromatin-immunoprecipitated DNA (ChIP-exo). The ChIP-exo has a unique peak-pair pattern indicating 5′ and 3′ ends of ArgR-binding region. We identified 62 ArgR-binding loci, which were classified into three groups, comprising single, double and triple peak-pairs. Each peak-pair has a unique 93 base pair (bp)-long (±2 bp) ArgR-binding sequence containing two ARG boxes (39 bp) and residual sequences. Moreover, the three ArgR-binding modes defined by the position of the two ARG boxes indicate that DNA bends centered between the pair of ARG boxes facilitate the non-specific contacts between ArgR subunits and the residual sequences. Additionally, our approach may also reveal other fundamental structural features of TF-DNA interactions that have implications for studying genome-scale transcriptional regulatory networks.</P>
Current Challenges in Bacterial Transcriptomics
Cho, Suhyung,Cho, Yoobok,Lee, Sooin,Kim, Jayoung,Yum, Hyeji,Kim, Sun Chang,Cho, Byung-Kwan Korea Genome Organization 2013 Genomics & informatics Vol.11 No.2
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.
Applications of CRISPR/Cas System to Bacterial Metabolic Engineering
Cho, Suhyung,Shin, Jongoh,Cho, Byung-Kwan MDPI 2018 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.19 No.4
<P>The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) adaptive immune system has been extensively used for gene editing, including gene deletion, insertion, and replacement in bacterial and eukaryotic cells owing to its simple, rapid, and efficient activities in unprecedented resolution. Furthermore, the CRISPR interference (CRISPRi) system including deactivated Cas9 (dCas9) with inactivated endonuclease activity has been further investigated for regulation of the target gene transiently or constitutively, avoiding cell death by disruption of genome. This review discusses the applications of CRISPR/Cas for genome editing in various bacterial systems and their applications. In particular, CRISPR technology has been used for the production of metabolites of high industrial significance, including biochemical, biofuel, and pharmaceutical products/precursors in bacteria. Here, we focus on methods to increase the productivity and yield/titer scan by controlling metabolic flux through individual or combinatorial use of CRISPR/Cas and CRISPRi systems with introduction of synthetic pathway in industrially common bacteria including <I>Escherichia coli</I>. Further, we discuss additional useful applications of the CRISPR/Cas system, including its use in functional genomics.</P>
Sang-Hyeok CHO,Yujin JEONG,Seong-Joo HONG,Hookeun LEE,Hyung-Kyoon CHOI,Dong-Myung KIM,Jaemin SEONG,Gahyeon KIM,Choul-Gyun LEE,Suhyung CHO,Byung-Kwan CHO 한국생물공학회 2021 한국생물공학회 학술대회 Vol.2021 No.4
Cyanobacteria are able to produce diverse value-added biochemicals from CO<sub>2</sub> and light. To utilize the potency, it is critical to understand the photosynthetic mechanism under various environmental conditions. Here, we investigated the inhibitory mechanisms of photosynthesis under high light and low temperature stress in Synechocystis sp. PCC 6803. Under each stress condition, the transcript abundance and translation efficiency were measured using RNA-seq and Ribo-seq, and the transcription unit architecture was constructed by transcription start sites and transcript 3'-end positions obtained from TSS-seq and Term-seq. Our results suggested that the mode of photosynthesis inhibition differed between the two stress conditions. The poor translation of photosystem I resulted from ribosome stalling at the untranslated regions, affecting the overall photosynthesis under low temperature. Our multi-omics analysis with transcription unit provides foundational information on photosynthesis for future industrial strain development.
( Sang-hyeok Cho ),( Yujin Jeong ),( Eunju Lee ),( So-ra Ko ),( Chi-yong Ahn ),( Hee-mock Oh ),( Byung-kwan Cho ),( Suhyung Cho ) 한국미생물생명공학회(구 한국산업미생물학회) 2021 Journal of microbiology and biotechnology Vol.31 No.4
Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pangenome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.