Dong Su Yu
Korea Research Institute of Bioscience and Biotechnology
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Publication
Featured researches published by Dong Su Yu.
Nature | 2009
Jeffrey E. Barrick; Dong Su Yu; Haeyoung Jeong; Tae Kwang Oh; Dominique Schneider; Richard E. Lenski; Jihyun F. Kim
The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.
Journal of Molecular Biology | 2009
Haeyoung Jeong; Valérie Barbe; Choong Hoon Lee; David Vallenet; Dong Su Yu; Sang Haeng Choi; Arnaud Couloux; Seung Won Lee; Laurence Cattolico; Cheol Goo Hur; Hong Seog Park; Béatrice Segurens; Sun Chang Kim; Tae Kwang Oh; Richard E. Lenski; F.William Studier; Patrick Daegelen; Jihyun F. Kim
Escherichia coli K-12 and B have been the subjects of classical experiments from which much of our understanding of molecular genetics has emerged. We present here complete genome sequences of two E. coli B strains, REL606, used in a long-term evolution experiment, and BL21(DE3), widely used to express recombinant proteins. The two genomes differ in length by 72,304 bp and have 426 single base pair differences, a seemingly large difference for laboratory strains having a common ancestor within the last 67 years. Transpositions by IS1 and IS150 have occurred in both lineages. Integration of the DE3 prophage in BL21(DE3) apparently displaced a defective prophage in the lambda attachment site of B. As might have been anticipated from the many genetic and biochemical experiments comparing B and K-12 over the years, the B genomes are similar in size and organization to the genome of E. coli K-12 MG1655 and have >99% sequence identity over approximately 92% of their genomes. E. coli B and K-12 differ considerably in distribution of IS elements and in location and composition of larger mobile elements. An unexpected difference is the absence of a large cluster of flagella genes in B, due to a 41 kbp IS1-mediated deletion. Gene clusters that specify the LPS core, O antigen, and restriction enzymes differ substantially, presumably because of horizontal transfer. Comparative analysis of 32 independently isolated E. coli and Shigella genomes, both commensals and pathogenic strains, identifies a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome.
Journal of Bacteriology | 2009
Jihyun F. Kim; Haeyoung Jeong; Dong Su Yu; Sang-Haeng Choi; Cheol-Goo Hur; Myeong-Soo Park; Dae Won Kim; Geun Eog Ji; Hong-Seog Park; Tae Kwang Oh
Bifidobacterium animalis subsp. lactis is a probiotic bacterium that naturally inhabits the guts of most mammals, including humans. Here we report the complete genome sequence of B. animalis subsp. lactis 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.
Journal of Bacteriology | 2010
Ju Yeon Song; Haeyoung Jeong; Dong Su Yu; Michael A. Fischbach; Hong-Seog Park; Jae Jong Kim; Jeong-Sun Seo; Susan E. Jensen; Tae Kwang Oh; Kye Joon Lee; Jihyun F. Kim
Streptomyces clavuligerus is an important industrial strain that produces a number of antibiotics, including clavulanic acid and cephamycin C. A high-quality draft genome sequence of the S. clavuligerus NRRL 3585 strain was produced by employing a hybrid approach that involved Sanger sequencing, Roche/454 pyrosequencing, optical mapping, and partial finishing. Its genome, comprising four linear replicons, one chromosome, and four plasmids, carries numerous sets of genes involved in the biosynthesis of secondary metabolites, including a variety of antibiotics.
Journal of Bacteriology | 2012
Ju Yeon Song; Hyun A. Kim; Ji Seoung Kim; Seon Young Kim; Haeyoung Jeong; Sung Gyun Kang; Byung Kwon Kim; Soon Kyeong Kwon; Choong Hoon Lee; Dong Su Yu; Beom Seok Kim; Sun Hyung Kim; Suk Yoon Kwon; Jihyun F. Kim
Volatile and nonvolatile compounds emitted from the plant growth-promoting rhizobacterium Bacillus sp. strain JS enhance the growth of tobacco and lettuce. Here, we report the high-quality genome sequence of this bacterium. Its 4.1-Mb genome reveals a number of genes whose products are possibly involved in promotion of plant growth or antibiosis.
Journal of Bacteriology | 2012
Byung Kwon Kim; Joon Hui Chung; Seon Young Kim; Haeyoung Jeong; Sung Gyun Kang; Soon Kyeong Kwon; Choong Hoon Lee; Ju Yeon Song; Dong Su Yu; Choong Min Ryu; Jihyun F. Kim
Plant growth-promoting bacteria colonize various habitats, including the phyllosphere. Here, we present the high-quality draft genome sequence of Bacillus sp. strain 5B6, which was isolated from the leaf of a cherry tree. The 3.9-Mb genome uncovers its potential for understanding the nature of leaf colonization as well as antibiosis against plant pathogens.
Journal of Bacteriology | 2012
Min-Jung Kwak; Ju Yeon Song; Seon-Young Kim; Haeyoung Jeong; Sung Gyun Kang; Byung Kwon Kim; Choong Hoon Lee; Dong Su Yu; Seung-Hwan Park; Jihyun F. Kim
Endophytes live inside plant tissues without causing any harm and may even benefit plants. Here, we provide the high-quality genome sequence of Burkholderia sp. strain KJ006, an endophytic bacterium of rice with antifungal activity. The 6.6-Mb genome, consisting of three chromosomes and a single plasmid, contains genes related to plant growth promotion or degradation of aromatic compounds.
Journal of Bacteriology | 2012
Dong Su Yu; Haeyoung Jeong; Dae-Hee Lee; Soon Kyeong Kwon; Ju Yeon Song; Byung Kwon Kim; Myeong Soo Park; Geun Eog Ji; Tae Kwang Oh; Jihyun F. Kim
Bifidobacterium bifidum, a common endosymbiotic inhabitant of the human gut, is considered a prominent probiotic microorganism that may promote health. We completely decrypted the 2.2-Mb genome sequence of B. bifidum BGN4, a strain that had been isolated from the fecal sample of a healthy breast-fed infant, and annotated 1,835 coding sequences.
Journal of Bacteriology | 2012
Haeyoung Jeong; Fumei Zhao; Davaajargal Igori; Kyung-Hwan Oh; Seon Young Kim; Sung Gyun Kang; Byung Kwon Kim; Soon Kyeong Kwon; Choong Hoon Lee; Ju Yeon Song; Dong Su Yu; Mi Sun Park; Seung Hak Cho; Jihyun F. Kim
Enterohemorrhagic Escherichia coli (EHEC) causes a disease involving diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome (HUS). Here we present the draft genome sequence of NCCP15647, an EHEC isolate from an HUS patient. Its genome exhibits features of EHEC, such as genes for verotoxins, a type III secretion system, and prophages.
Journal of Bacteriology | 2012
Byung Kwon Kim; Seong Hyuk Lee; Seon Young Kim; Haeyoung Jeong; Soon Kyeong Kwon; Choong Hoon Lee; Ju Yeon Song; Dong Su Yu; Sung Gyun Kang; Jihyun F. Kim
Thermococcus zilligii, a thermophilic anaerobe in freshwater, is useful for physiological research and biotechnological applications. Here we report the high-quality draft genome sequence of T. zilligii AN1(T). The genome contains a number of genes for an immune system and adaptation to a microbial biomass-rich environment as well as hydrogenase genes.
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Korea Research Institute of Bioscience and Biotechnology
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