• Genomics & Informatics
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• v.3 no.4
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• pp.142-148
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• 2005

The immune response-related genes have been suggested to be the most favorable genes for positive selection during evolution. Comparing the entire DNA sequence of chimpanzee chromosome 22 (PTR22) with human chromosome 21 (HSA21), we have identified 15 orthologs having indel in their coding sequences. Among them, interferon-${\alpha}$ receptor-1 gene (IFNAR1), an immuneresponse-related gene, is subjected to comparative genomic analysis. Chimpanzee IFNAR1 showed the same genomic structure as human IFNAR1 (11 exons and 10 introns) except the 3 bp insertion in exon 4. The sequence alignment of IFNAR1 coding sequence indicated that 'ISPP' amino acid sequence motif is highly conserved in chimpanzee and other animals including mouse and chicken. However, the human IFNAR1 shows that one proline residue is missing in the sequence motif. The homology modeling of the IFNAR1 structures suggests that the proline deletion in human IFNAR1 leads to the formation of the following ${\alpha}$-helix, whereas two sequential prolines in chimpanzee IFNAR1 inhibit it. As a result, human IFNAR1 may adopt a characteristic structure distinct from chimpanzee IFNAR1. This human specific trait could contribute to specific immune response in the most optimized manner for humans. Further molecular biological studies on the IFNAR1 will help us to gain insights into the molecular implication of species-specific host-pathogen interaction in primate evolution.

• The Korean Journal of Pharmacology
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• v.24 no.1
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• pp.1-10
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• 1988

To obtain information about the structure of the human phenylethanolamin N-methyltransferase (PNMT) and to further define the extent of the evolutionary relationships among PNMT molecules of several spesies, a full length cDNA clone for bovine adrenal PNMT was used to screen a charon 4A genomic library. One phage was isolated and identified, which included the entire PNMT gene. The length of inserted genomic DNA was 13.1-Kilobase (Kb) containing two internal EcoRI sites. Construction of a restriction map and subsequent Southern and dot blot analysis with 5'-and3'-specific cDNA probes allowed the identification of exon-containing fragments. This is the first report of the cloning of gene for human epinephrine synthesizing enzyme.

• Molecules and Cells
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• v.44 no.7
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• pp.458-467
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• 2021

GPR43 (also known as FFAR2 or FFA2) is a G-protein-coupled receptor primarily expressed in immune cells, enteroendocrine cells and adipocytes that recognizes short-chain fatty acids, such as acetate, propionate, and butyrate, likely to be implicated in innate immunity and host energy homeostasis. Activated GPR43 suppresses the cAMP level and induces Ca²⁺ flux via coupling to Gα_i and Gα_q families, respectively. Additionally, GPR43 is reported to facilitate phosphorylation of ERK through G-protein-dependent pathways and interacts with β-arrestin 2 to inhibit NF-κB signaling. However, other G-protein-dependent and independent signaling pathways involving GPR43 remain to be established. Here, we have demonstrated that GPR43 augments Rho GTPase signaling. Acetate and a synthetic agonist effectively activated RhoA and stabilized YAP/TAZ transcriptional coactivators through interactions of GPR43 with Gα_q/11 and Gα_12/13. Acetate-induced nuclear accumulation of YAP was blocked by a GPR43-specific inverse agonist. The target genes induced by YAP/TAZ were further regulated by GPR43. Moreover, in THP-1-derived M1-like macrophage cells, the Rho-YAP/TAZ pathway was activated by acetate and a synthetic agonist. Our collective findings suggest that GPR43 acts as a mediator of the Rho-YAP/TAZ pathway.

• International Journal of Industrial Entomology and Biomaterials
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• v.25 no.1
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• pp.99-110
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• 2012

Comparison on the genomic structure and phylogenetic relationship of the Hsp88 genes from P. tenuipes Jochoen-1, P. tenuipes, C. militaris and C. pruinosa was described. The Hsp88 genes from the three entomopathogenic strains, P. tenuipes Jocheon-1(strain), P. tenuipes(original species), and C. militaris contain the identical genomic structure, namely 5 introns and 6 exons with the length of 13, 62, 32, 1,438, 306, 288 nucleotides encoding 713 amino acid residues, whereas in case of C. pruinosa, it contains 4 introns and 5 exons with the length of 13, 62, 32, 1,744, 288 nucleotides encoding 713 amino acid residues. The genomic DNA length of the Hsp88 genes from P. tenuipes Jocheon-1 and P. tenuipes are both 2,600 nucleotides long in size. The Hsp88 genes from C. militaris and C. pruinosa are 2,582, 2,576 nucleotides long in size, respectively. Hsp88 genes of the P. tenuipes Jochoen-1, P. tenuipes, C. militaris and C. pruinosa also contain the conserved ATP-binding domain. Phylogenetic analysis of the Hsp genes of the four strains tested in this study showed that the fungal Hsp88 is divided into two separate clades, ascomycetes and deutromycete. Within the ascomycetes fungal clade, the P. tenuipes Jochoen-1 and P. tenuipes formed a subgroup, on the other hand, C. militaris and C. pruinosa formed another subgroup. Pair-wise comparison of P. tenuipes Jocheon-1 Hsp88 with those of P. tenuipes, C. militaris and C. pruinosa Hsp88s revealed significant identity in deduced amino acid sequence among these strains. The P. tenuipes Jocheon-1 Hsp88 showed 99% identity with the P. tenuipes, 97% identity with the C. militaris, and 98% identity with the C. pruinosa.

• BMB Reports
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• v.49 no.12
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• pp.653-654
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• 2016

The human reference genome, maintained by the Genome Reference Consortium, is conceivably the most complete genome assembly ever, since its first construction. It has continually been improved by incorporating corrections made to the previous assemblies, thanks to various technological advances. Many currently-ongoing population sequencing projects have been based on this reference genome, heightening hopes of the development of useful medical applications of genomic information, thanks to the recent maturation of high-throughput sequencing technologies. However, just one reference genome does not fit all the populations across the globe, because of the large diversity in genomic structures and technical limitations inherent to short read sequencing methods. The recent success in de novo construction of the highly contiguous Asian diploid genome AK1, by combining single molecule technologies with routine sequencing data without resorting to traditional clone-by-clone sequencing and physical mapping, reveals the nature of genomic structure variation by detecting thousands of novel structural variations and by finally filling in some of the prior gaps which had persistently remained in the current human reference genome. Now it is expected that the AK1 genome, soon to be paired with more upcoming de novo assembled genomes, will provide a chance to explore what it is really like to use ancestry-specific reference genomes instead of hg19/hg38 for population genomics. This is a major step towards the furthering of genetically-based precision medicine.

• Molecules and Cells
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• v.19 no.3
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• pp.303-309
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• 2005

The end of eukaryotic genomic DNA is capped by a specialized structure called as "telomere" which consists of the repetitive array of nucleotide sequence, TTAGGG, in humans and mice, and a variety of binding proteins. Telomerase is a ribonucleoprotein (RNP) complex responsible for the elongation of telomeres to maintain the genomic integrity, and is composed of telomerase reverse transcriptase (TERT), telomerase RNA component (TERC), and their associated factors regulating the catalytic activity of telomerase. Although it is now apparent that telomerase protects cells from apoptosis via the maintenance of genomic integrity by stabilizing telomeres, our understanding for the physiological role of telomerase is yet far from completion, and emerging evidence suggests that telomerase has additional extratelomeric roles in mediating cell survival and anti-apoptotic functions against various cytotoxic stresses. Here we summarize and discuss how telomerase and telomeres are involved in mediating cellular protection against apoptosis.

• Journal of Microbiology and Biotechnology
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• v.9 no.4
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• pp.404-413
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• 1999

Methanopyrus kandleri is a hyperthermophilic methanogen that represents one of the most heat-resistant organisms: the maximum growth temperature of M. kandleri is $110^{\circ}C$. A random sequence analysis of the genomic DNA of M. kandleri has been performed to obtain genomic information. More than 200 unique sequence tags were obtained and compared with the sequences in the GenBank and PIR databases. About 30% of the analyzed tags showed strong sequence similarity to previously identified genes involved in various cellular processes such as biosynthesis, transport, methanogenesis, or metabolism. When statistics relating to the frequency of codons were examined, the sequenced open reading frames showed highly biased codon usage and a high content of charged amino acids. Among the identified genes, a homologue of the catalytic subunit of carbon monoxide dehydrogenase (CODH) that reduces $CO_2$ to CO was cloned and sequenced in order to examine its detailed gene structure. The cloned gene includes consensus promoters. The amino acid sequence of the cloned gene shows a strong homology with the CODH genes from methanogenic Archaea, especially in the presumed binding sites for Fe-S centers.

• Journal of Science and Technology Studies
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• v.15 no.1
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• pp.145-180
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• 2015

Human Genome Project was a big science done by United States, U.K., France, China, Germany and Japan. But in Korea HGP was not constructed because of lack of governmental funding and failure to attract relevant actors' attention in spite of small voices from early genome researchers and some family members of patients with incurable diseases. This article does not argue that HGP in Korea was an undone science, a concept claimed by Scott Frickel, et al. Instead, it shows the historical fact that HGP was not constructed in Korea in 1990s and analyzes how genomic researches could become possible in Korea in the post-genomic age using the framework of triple-helix. In Korea, researchers have constructed hybrid networks and organizations that intermingles laboratories of university, industry, and government to conduct genomic researches which requires a lot of financial funding. This structure is different from the entrepreneurial university seen in developed countries such as the United States. Using two examples, this article shows that founding a start-up company by university researchers was not an option as in the United States, but a necessity in order to obtain enough funding to conduct genomic researches in Korea. Otherwise, researchers in Korean universities had to form hybrid networks with government to obtain small amount of funds to conduct researches. I argue that this phenomenon shows multifaceted characteristics of institutional structures regarding genomic researches in Korea.

• International Journal of Industrial Entomology and Biomaterials
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• v.14 no.1
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• pp.51-56
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• 2007

In a previous study, three larval cuticle protein genes were cloned from the mulberry longicorn beetle, Apriona germari (Comp. Biochem. Physiol. B 136, 803-811, 2003). In the present study, the genomic structures of these three larval cuticle protein genes (AgLCP9.2, AgLCP12.6 and AgLCP12.3) were elucidated. All three cuticle protein genes consist of one intron and two exons. Southern blot analysis of genomic DNA suggested that three cuticle protein genes are a single copy gene. In addition, a novel larval cuticle protein gene, AgLCP10.6, was cloned from A. germari in this study. The AgLCP10.6 cDNA contains an ORF of 300 nucleotides that are capable of encoding a 100-amino acid polypeptide with a predicted molecular mass of 10.6 kDa. The amino acid sequence deduced from the AgLCP10.6 cDNA contained a type-specific consensus sequence identifiable in other insect cuticle proteins and is most homologous to Drosophila melanogaster cuticle protein ACP65A (51 % protein sequence identity). Northern blot analysis revealed that AgLCP10.6 showed epidermis-specific expression.

• Korean Journal of Plant Tissue Culture
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• v.28 no.5
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• pp.255-261
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• 2001

Vitis vinifera thaumatin-like protein (VVTL1) is a fruit-specific and ripening-related protein in grape. In order to isolate VVTL1-homolog gene and fruit-specific promoter from Campbell cultivar, we isolated a genomic clone containing VVTL1-homolog gene from grape genomic library through plaque hybridization. VVTL1-homolog gene has an intronless genomic structure, which the pattern is matched with those of other PR5 genes such as osmotin and osmotin-like protein genes. Transcription start site was determined by primer extension analysis. The promoter region of VVTL1-homolog gene contains a sequence or structure, especially the location and number of TCA box and ABRE (abscisic acid-responsive element), distinct from other reported plant PR5 genes, though with several known functional elements such as a TATA box and CAAT box. These results suggested that VVTL1-homolog gene may be regulated by a plant hormone, abscisic acid, and one or several stresses such osmotic pressure and pathogen infection. The isolation of fruit-specific promoter may be helpful to breed a genetically modified grape with valuable phenotype or materials in fruits.