• Proceedings of the Microbiological Society of Korea Conference
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• 2009.05a
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• pp.148-149
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• 2009

• The Journal of the Korean Society for Microbiology
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• v.34 no.6
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• pp.519-532
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• 1999

Helicobacter pylori is a causative agent of type B gastritis and plays a central role in the pathogenesis of gastroduodenal ulcer and gastric cancer. To elucidate the host-parasite relationship of the H. pylori infection on the basis of molecular biology, we tried to evaluate the genomic diversity of H. pylori. An ordered overlapping bacterial artificial chromosome (BAC) library of a Korean isolate, H. pylori 51 was constructed to set up a genomic map. A circular physical map was constructed by aligning ApaI, NotI and SfiI-digested chromosomal DNA. When the physical map of H. pylori 51 was compared to that of unrelated strain, H. pylori 26695, completely different restriction patterns were shown. Fifteen known genes were mapped on the chromosome of H. pylori 51 and the genetic map was compared with those of strain 26695 and J99, of which the entire genomic sequences were reported. There were some variability in the gene location as well as gene order among three strains. For further analysis on the genomic diversity of H. pylori, when comparing the genomic structure of 150 H. pylori Korean isolates with one another, genomic macrodiversity of H. pylori was characterized by several features: whether or not susceptible to restriction digestion of the chromsome, variation in chromosomal restriction fingerprint and/or high frequency of gene rearrangement. We also examined the extent of allelic variation in nucleotide or deduced amino acid sequences at the individual gene level. fucT, cagA and vacA were confirmed to carry regions of high variation in nucleotide sequence among strains. The plasticity zone and strain-specific genes of H. pylori 51 were analyzed and compared with the former two genomic sequences. It should be noted that the H. pylori 51-specific sequences were dispersed on the chromosome, not congregated in the plasticity zone unlike J99- or 26695-specific genes, suggesting the high frequency of gene rearrangement in H. pylori genome. The genome of H. pylori 51 shows differences in the overall genomic organization, gene order, and even in the nucleotide sequences among the H. pylori strains, which are far greater than the differences reported on the genomic diversity of H. pylori.

• IMMUNE NETWORK
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• v.23 no.1
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• pp.5.1-5.28
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• 2023

Th cell lineage determination and functional specialization are tightly linked to the activation of lineage-determining transcription factors (TFs) that bind cis-regulatory elements. These lineage-determining TFs act in concert with multiple layers of transcriptional regulators to alter the epigenetic landscape, including DNA methylation, histone modification and threedimensional chromosome architecture, in order to facilitate the specific Th gene expression programs that allow for phenotypic diversification. Accumulating evidence indicates that Th cell differentiation is not as rigid as classically held; rather, extensive phenotypic plasticity is an inherent feature of T cell lineages. Recent studies have begun to uncover the epigenetic programs that mechanistically govern T cell subset specification and immunological memory. Advances in next generation sequencing technologies have allowed global transcriptomic and epigenomic interrogation of CD4+ Th cells that extends previous findings focusing on individual loci. In this review, we provide an overview of recent genome-wide insights into the transcriptional and epigenetic regulation of CD4+ T cell-mediated adaptive immunity and discuss the implications for disease as well as immunotherapies.

• Journal of Microbiology and Biotechnology
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• v.13 no.5
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• pp.783-788
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• 2003

A 27 bp $tRNA^{Gly}$ region (att1) was identified as the integration site for a 12,384 bp Pfl-derived genomic island containing 15 open reading frames (ORFs) from PA0715 to PA0729 in P. aeruginosa strain PAOl. Homologous island was observed in P. aeruginosa strain PA14, but not in P. aeruginosa strain K (PAK). We isolated the Pfl island from PA14, and determined its 10,657 bp sequences containing 14 ORFs, with significant sequence variations near the borders. In contrast to the PAO1 Pfl island, the PA14 Pfl island was integrated at the 10 bp att2 site between PA1191 and PA1192. The attl site of PA14, however, was still occupied by a third genetic segment, whereas both attl and att2 sites of PAK remained unutilized. These results exemplify an extensive genomic variation of Pfl-related islands involving differential genetic organizations and differential att site utilizations.

• Journal of Microbiology and Biotechnology
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• v.15 no.4
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• pp.844-854
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• 2005

We constructed a defined physical and genetic map of H. pylori strain 51, previously isolated from a Korean patient with a duodenal ulcer, by combining a restriction analysis by pulse-field gel electrophoresis with the construction of a BAC library. A Notl-digest of H. pylori strain 51 genome yielded seven fragments, from which the genomic size was estimated to be 1,698$\pm$24 kb. The BAC library was constructed from 50 to 200 kb fragments of HindIII-digested genomic DNA. From 700 BAC clones, an ordered overlapping maxi-set of 82 BAC clones was assembled that covered the entire genome. The positions of 15 genes were localized in the strain 51 genome with 4-22 kb of resolution and were compared with their orthologues in strain 26695 and strain J99. The arrangement of the 15 genes was identical in strain 51 and strain J99, except for flaA and hpaA. The plasticity zone of strain 51, like that of strain J99, was located in the single region, and was shorter than those of strain 26695 and strain J99. The strain 51 plasticity zone consisted of ORFs common only to strain 51 and J99 or to strain 51 and 26695, as well as strain 51-specific ORFs. Three genetic translocations and/or inversions were found between orthologue ORFs in strain 51 and strain J99. These results show that the chromosomal organization of strain 51 differs from Western strains such as strain 26695 and strain J99.

• Journal of Life Science
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• v.10 no.1
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• pp.32-36
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• 2000

Solitary long terminal repeats(LTRs) of human endogenous retrovirus K family(HERV-K) have been found to be coexpressed with sequences of closely located genes. It has been suggested that HERV-K LTR-like elements entered the primate genome approximately 33-40 million years ago. WE investigated the presence of HERV-K LTR elements in New World monkeys using PCR amplification. Six LTR elements of HERV-K family were identified from New World monkeys, represented by the squirrel and night monkeys. They showed a high degree of sequence homology(96-99%) with the human-specific HERV-K LTR elements. Phylogenetic analysis reveals that an LTR element (SM-1) from the squirrel monkey and another LTR element (NM-1) from the night monkey are very closely related to the human-specific HERV-K LTR elements with low degree of divergence. This finding suggests that some of LTR elements of HERV-K family have recently been proliferated in New World monkeys. A sequence in chromosome Xq26(AL034407) \ulcorner contains an HERV-K LTR element was shown to be present in the human genome, but is absent in the bonobo, chimpanzee, gorilla, orangutan, and gibbon. It has more than 99% homology to other human-specific HERV-K LTR elements. This sequence thus represents and isolated insertion of an evolving class of elements that may have made a particular contribution to human genomic plasticity.

• Animal Bioscience
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• v.37 no.2_spc
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• pp.396-403
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• 2024

Objective: Monofluoroacetate (MFA) is a potent toxin that blocks ATP production via the Krebs cycle and causes acute toxicity in ruminants consuming MFA-containing plants. The rumen bacterium, Cloacibacillus porcorum strain MFA1 belongs to the phylum Synergistota and can produce fluoride and acetate from MFA as the end-products of dehalorespiration. The aim of this study was to identify the genomic basis for the metabolism of MFA by this bacterium. Methods: A draft genome sequence for C. porcorum strain MFA1 was assembled and quantitative transcriptomic analysis was performed thus highlighting a candidate operon encoding four proteins that are responsible for the carbon-fluorine bond cleavage. Comparative genome analysis of this operon was undertaken with three other species of closely related Synergistota bacteria. Results: Two of the genes in this operon are related to the substrate-binding components of the glycine reductase protein B (GrdB) complex. Glycine shares a similar structure to MFA suggesting a role for these proteins in binding MFA. The remaining two genes in the operon, an antiporter family protein and an oxidoreductase belonging to the radical S-adenosyl methionine superfamily, are hypothesised to transport and activate the GrdB-like protein respectively. Similar operons were identified in a small number of other Synergistota bacteria including type strains of Cloacibacillus porcorum, C. evryensis, and Pyramidobacter piscolens, suggesting lateral transfer of the operon as these genera belong to separate families. We confirmed that all three species can degrade MFA, however, substrate degradation in P. piscolens was notably reduced compared to Cloacibacillus isolates possibly reflecting the loss of the oxidoreductase and antiporter in the P. piscolens operon. Conclusion: Identification of this unusual anaerobic fluoroacetate metabolism extends the known substrates for dehalorespiration and indicates the potential for substrate plasticity in amino acid-reducing enzymes to include xenobiotics.