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총설 : 차세대 유전체 기술과 환경생물학 -환경유전체학 시대를 맞이하여
송주연 ( Ju Yeon Song ),김병권 ( Byung Kwon Kim ),권순경 ( Soon Kyeong Kwon ),곽민정 ( Min Jung Kwak ),김지현 ( Jihyun F Kim ) 한국환경생물학회 2012 환경생물 : 환경생물학회지 Vol.30 No.2
With the advent of the genomics era powered by DNA sequencing technologies, life science is being transformed significantly and biological research and development have been accelerated. Environmental biology concerns the relationships among living organisms and their natural environment, which constitute the global biogeochemical cycle. As sustainability of the ecosystems depends on biodiversity, examining the structure and dynamics of the biotic constituents and fully grasping their genetic and metabolic capabilities are pivotal. The high-speed highthroughput next-generation sequencing can be applied to barcoding organisms either thriving or endangered and to decoding the whole genome information. Furthermore, diversity and the full gene complement of a microbial community can be elucidated and monitored through metagenomic approaches. With regard to human welfare, microbiomes of various human habitats such as gut, skin, mouth, stomach, and vagina, have been and are being scrutinized. To keep pace with the rapid increase of the sequencing capacity, various bioinformatic algorithms and software tools that even utilize supercomputers and cloud computing are being developed for processing and storage of massive data sets. Environmental genomics will be the major force in understanding the structure and function of ecosystems in nature as well as preserving, remediating, and bioprospecting them.
Kwak, Min-Jung,Lee, Jung-Sook,Lee, Keun Chul,Kim, Kwang Kyu,Eom, Mi Kyung,Kim, Byung Kwon,Kim, Jihyun F. International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.11
<P>Four Gram-stain-negative, aerobic, rod-shaped bacterial strains, MM-124, MM-126, NB-68 and NB-77, were isolated from the coastal seawater or a region with a bloom of sea sparkle around Geoje island in Korea. The sequence similarity values of the 16S rRNA gene between the isolates and <I>Sulfitobacter mediterraneus</I> DSM 12244<SUP>T</SUP> ranged from 97.7 to 98.2 %, and phylogenetic relationships suggested that they belong to a phylogenetic branch that includes the genera <I>Sulfitobacter</I> and <I>Roseobacter</I>. The isoprenoid quinone of all three novel strains was ubiquinone-10 and the major fatty acid was <I>cis</I>-vaccenic acid, as in other species of the genus <I>Sulfitobacter</I>. However, there were several differences in the morphological, physiological and biochemical characteristics among the four strains and the reference species of the genus <I>Sulfitobacter</I>. Moreover, the average nucleotide identity values between the three sequenced isolates and the reference strains were below 76.33, indicating that genomic variation exists between the isolates and reference strains. Chemotaxonomic characteristics together with phylogenetic affiliations and genomic distances illustrate that strains MM-124, NB-68 and NB-77 represent novel species of the genus <I>Sulfitobacter</I>, for which the names <I>Sulfitobacter</I> g<I>eojensis</I> sp. nov. (type strain MM-124<SUP>T</SUP> = KCTC 32124<SUP>T</SUP> = JCM 18835<SUP>T</SUP>), <I>Sulfitobacter noctilucae</I> sp. nov. (type strain NB-68<SUP>T</SUP> = KCTC 32122<SUP>T</SUP> = JCM 18833<SUP>T</SUP>) and <I>Sulfitobacter noctilucicola</I> sp. nov. (type strain NB-77<SUP>T</SUP> = KCTC 32123<SUP>T</SUP> = JCM 18834<SUP>T</SUP>) are proposed.</P>
Complete Genome Sequence of Leuconostoc citreum KM20
Kim, Jihyun F.,Jeong, Haeyoung,Lee, Jung-Sook,Choi, Sang-Haeng,Ha, Misook,Hur, Cheol-Goo,Kim, Ji-Sun,Lee, Soohyun,Park, Hong-Seog,Park, Yong-Ha,Oh, Tae Kwang American Society for Microbiology 2008 Journal of Bacteriology Vol.190 No.8
<B>ABSTRACT</B><P><I>Leuconostoc citreum</I> is one of the most prevalent lactic acid bacteria during the manufacturing process of kimchi, the best-known Korean traditional dish. We have determined the complete genome sequence of <I>L. citreum</I> KM20. It consists of a 1.80-Mb chromosome and four circular plasmids and reveals genes likely involved in kimchi fermentation and its probiotic effects.</P>
Genome Sequence of the Probiotic Bacterium Bifidobacterium animalis subsp. lactis AD011
Kim, Jihyun F.,Jeong, Haeyoung,Yu, Dong Su,Choi, Sang-Haeng,Hur, Cheol-Goo,Park, Myeong-Soo,Yoon, Sung Ho,Kim, Dae-Won,Ji, Geun Eog,Park, Hong-Seog,Oh, Tae Kwang American Society for Microbiology 2009 Journal of Bacteriology Vol.191 No.2
<B>ABSTRACT</B><P><I>Bifidobacterium animalis</I> subsp. <I>lactis</I> is a probiotic bacterium that naturally inhabits the guts of most mammals, including humans. Here we report the complete genome sequence of <I>B. animalis</I> subsp. <I>lactis</I> AD011 that was isolated from an infant fecal sample. Biological functions encoded in a single circular chromosome of 1,933,695 bp, smallest among the completely sequenced bifidobacterial genomes, are suggestive of their probiotic functions, such as utilization of bifidogenic factors and a variety of glycosidic enzymes and biosynthesis of polysaccharides.</P>
Genome Sequence of the Thermotolerant Yeast Kluyveromyces marxianus var. <i>marxianus</i> KCTC 17555
Jeong, Haeyoung,Lee, Dae-Hee,Kim, Sun Hong,Kim, Hyun-Jin,Lee, Kyusang,Song, Ju Yeon,Kim, Byung Kwon,Sung, Bong Hyun,Park, Jae Chan,Sohn, Jung Hoon,Koo, Hyun Min,Kim, Jihyun F. American Society for Microbiology 2012 EUKARYOTIC CELL Vol.11 No.12
<B>ABSTRACT</B><P>Kluyveromyces marxianus is a thermotolerant yeast that has been explored for potential use in biotechnological applications, such as production of biofuels, single-cell proteins, enzymes, and other heterologous proteins. Here, we present the high-quality draft of the 10.9-Mb genome of K. marxianus var. <I>marxianu</I> s KCTC 17555 (= CBS 6556 = ATCC 26548). </P>
High Dose $^{60}Co\;{\gamma}$-Ray Irradiation of W/GaN Schottky Diodes
Kim, Jihyun,Ren, F.,Schoenfeld, D.,Pearton, S.J.,Baca, A.G.,Briggs, R.D. The Institute of Electronics and Information Engin 2004 Journal of semiconductor technology and science Vol.4 No.2
W/n-GaN Schottky diodes were irradiated with $^{60}Co\;{\gamma}-rays$ to doses up to 315Mrad. The barrier height obtained from current-voltage (I-V) measurements showed minimal change from its estimated initial value of ${\sim}0.4eV$ over this dose range, though both forward and reverse I-V characteristics show evidence of defect center introduction at doses as low as 150 Mrad. Post irradiation annealing at $500^{\circ}C$ increased the reverse leakage current, suggesting migration and complexing of defects. The W/GaN interface is stable to high dose of ${\gamma}-rays$, but Au/Ti overlayers employed for reducing contact sheet resistance suffer from adhesion problems at the highest doses.
Kim, Jihyun F.,Jeong, Haeyoung,Park, Soo-Young,Kim, Seong-Bin,Park, Yon Kyoung,Choi, Soo-Keun,Ryu, Choong-Min,Hur, Cheol-Goo,Ghim, Sa-Youl,Oh, Tae Kwang,Kim, Jae Jong,Park, Chang Seuk,Park, Seung-Hwan American Society for Microbiology 2010 Journal of Bacteriology Vol.192 No.22
<B>ABSTRACT</B><P><I>Paenibacillus polymyxa</I> E681, a spore-forming, low-G+C, Gram-positive bacterium isolated from the rhizosphere of winter barley grown in South Korea, has great potential for agricultural applications due to its ability to promote plant growth and suppress plant diseases. Here we present the complete genome sequence of <I>P. polymyxa</I> E681. Its 5.4-Mb genome encodes functions specialized to the plant-associated lifestyle and characteristics that are beneficial to plants, such as the production of a plant growth hormone, antibiotics, and hydrolytic enzymes.</P>
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>
Lee, Youngjin,Kim, Byoung Sik,Choi, Sanghyeon,Lee, Eun-Young,Park, Shinhye,Hwang, Jungwon,Kwon, Yumi,Hyun, Jaekyung,Lee, Cheolju,Kim, Jihyun F.,Eom, Soo Hyun,Kim, Myung Hee National Academy of Sciences 2019 Proceedings of the National Academy of Sciences Vol.116 No.36
<P><B>Significance</B></P><P>MARTX toxins present across multiple bacterial genera are primary virulence factors that facilitate initial colonization, dissemination, and lethality in a wide range of hosts, including humans. Upon entry into host cells, the toxins undergo a processing event to release their disease-related modularly structured effector domains. However, the mechanisms underlying processing and activation of diverse effector domains within the toxins remain unclear. Here, we use biochemical and structural biological approaches, in combination with cellular microbiological experiments, to demonstrate how Makes caterpillars floppy-like effector (MCF) or its homolog-containing MARTX toxins process effector modules and fully activate effectors. MCF-containing toxins target ADP-ribosylation factor proteins ubiquitously expressed in cells to activate and disseminate effectors across subcellular compartments simultaneously, eventually leading to systemic pathogenicity.</P><P>Upon invading target cells, multifunctional autoprocessing repeats-in-toxin (MARTX) toxins secreted by bacterial pathogens release their disease-related modularly structured effector domains. However, it is unclear how a diverse repertoire of effector domains within these toxins are processed and activated. Here, we report that Makes caterpillars floppy-like effector (MCF)-containing MARTX toxins require ubiquitous ADP-ribosylation factor (ARF) proteins for processing and activation of intermediate effector modules, which localize in different subcellular compartments following limited processing of holo effector modules by the internal cysteine protease. Effector domains structured tandemly with MCF in intermediate modules become disengaged and fully activated by MCF, which aggressively interacts with ARF proteins present at the same location as intermediate modules and is converted allosterically into a catalytically competent protease. MCF-mediated effector processing leads ultimately to severe virulence in mice via an MCF-mediated ARF switching mechanism across subcellular compartments. This work provides insight into how bacteria take advantage of host systems to induce systemic pathogenicity.</P>
Algorithm for Predicting Functionally Equivalent Proteins from BLAST and HMMER Searches
( Yu Dong Su ),( Dae Hee Lee ),( Seong Keun Kim ),( Choong Hoon Lee ),( Ju Yeon Song ),( Eun Bae Kong ),( Jihyun F Kim1 ) 한국미생물 · 생명공학회 2012 Journal of microbiology and biotechnology Vol.22 No.8
In order to predict biologically significant attributes such as function from protein sequences, searching against large databases for homologous proteins is a common practice. In particular, BLAST and HMMER are widely used in a variety of biological fields. However, sequencehomologous proteins determined by BLAST and proteins having the same domains predicted by HMMER are not always functionally equivalent, even though their sequences are aligning with high similarity. Thus, accurate assignment of functionally equivalent proteins from aligned sequences remains a challenge in bioinformatics. We have developed the FEP-BH algorithm to predict functionally equivalent proteins from protein-protein pairs identified by BLAST and from protein-domain pairs predicted by HMMER. When examined against domain classes of the Pfam-A seed database, FEP-BH showed 71.53% accuracy, whereas BLAST and HMMER were 57.72% and 36.62%, respectively. We expect that the FEP-BH algorithm will be effective in predicting functionally equivalent proteins from BLAST and HMMER outputs and will also suit biologists who want to search out functionally equivalent proteins from among sequence-homologous proteins.