• Journal of Life Science
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• v.11 no.2
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• pp.126-134
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• 2001

The phylogenetic tree displayed the presence of five groups in the Phellinus genus, which were distinguished based on their morphology. Most of the p. linteus appeared a cluster which was highly significant with the exception of P. linteus KACC 500122 and KACC 500411. They formed the sister taxa of P 1inteus where P. baumii, Phellinus sp. MPNU 7003, MPNU 7007, and MPNU 7010 had similar morphological characteristics. Also, P. nigricans IMSNU 32024 and P. pini var, carniformans IMSNU 32031 were grouped in the same cluster with P. igniarius KCTC 6227, KCTC 6228, and P. chrysoloma KCTC 6225 extracted from the Gen-Bank database. P. torulosus IMSNU 32028 and Phellinus sp. MPNU 7011 formed a closed group, however, these species had a distant taxa when compared with the other Phellinus species. The nucleotide sequences of the internal transcribed spacer (ITS) regions of ribosomal DNA (rDNA) including the 5.85 rDNA were determined from 24 strains of the Phellinus genus in order to analyze their phylogenetic relationship. These fungi were divided into two basic groups based on their ITS length, however, this grouping was different from that based on their morphological characteristics. Although various ITS sequences were ambiguously aligned, conserved sites were also identified. Accordingly, a neighbor-joining tree was constructed using the nucleotide sequence data of the conserved sites of the ITS regions and the 5.8S rDNA.

• Molecules and Cells
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• v.43 no.6
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• pp.572-580
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• 2020

Transient receptor potential ankyrin 1 from rattlesnakes (rsTRPA1) and boas (bTRPA1) was previously proposed to underlie thermo-sensitive infrared sensing based on transcript enrichment in infrared-sensing neurons and hyper-thermosensitivity expressed in Xenopus oocytes. It is unknown how these TRPA1s show thermosensitivities that overwhelm other thermoreceptors, and why rsTRPA1 is more thermosensitive than bTRPA1. Here, we show that snake TRPA1s differentially require Ca²⁺ for hyper-thermosensitivity and that predisposition to cytosolic Ca²⁺ potentiation correlates with superior thermosensitivity. Extracellularly applied Ca²⁺ upshifted the temperature coefficients (Q10s) of both TRPA1s, for which rsTRPA1, but not bTRPA1, requires cytosolic Ca²⁺. Intracellular Ca²⁺ chelation and substitutive mutations of the conserved cytosolic Ca²⁺-binding domain lowered rsTRPA1 thermosensitivity comparable to that of bTRPA1. Thapsigargin-evoked Ca²⁺ or calmodulin little affected rsTRPA1 activity or thermosensitivity, implying the importance of precise spatiotemporal action of Ca²⁺. Remarkably, a single rattlesnake-mimicking substitution in the conserved but presumably dormant cytosolic Ca²⁺-binding domain of bTRPA1 substantially enhanced thermosensitivity through cytosolic Ca²⁺ like rsTRPA1, indicating the capability of this single site in the determination of both cytosolic Ca²⁺ dependence and thermosensitivity. Collectively, these data suggest that Ca²⁺ is essential for the hyper-thermosensitivity of these TRPA1s, and cytosolic potentiation by permeating Ca²⁺ may contribute to the natural variation of infrared senses between rattlesnakes and boas.

• Fisheries and Aquatic Sciences
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• v.1 no.2
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• pp.227-231
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• 1998

The teleosts represent ancient real-bony vertebrates in phylogeny and resemble major genetic patterns to higher vertebrates. In the present study, we have defined the single family of insulin-like growth factors (IGFs) from flounder (Paralichthys olivaceus), compared to the prototype of IGFs observed in the Agnathan hagfish. In flounder, IGFs are clearly diverged into two major types including type I and II, and they are structurally similar by displaying a multidomain structure consisting of five functional regions as previously found in other vertebrates. However, flIGF-I appears to be more basic (pI 8.03) than the flIGF-II (pI 5.34) in the fully processed form for the B to D domain region. The flIGF-I seems to contain an evolutionary conserved Asn-linked glycosylation in E domain, which is not found in flIGF­II. The most interesting feature is that flIGF-II appeared to be structurally close to hagfish IGF in secondary structures, particularly in Band D domains. This could tell us an idea on the molecular divergence of IGFs from the Agnatha to teleosts during the vertebrate phylogeny. It also support, in part, a notion regarding on how IGF-II is appeared as more embryonic during development. Nonetheless, the biologically active B to D domain region of flIGF-II shows significant sequence homology of $65.6\%$ to flIGF-Is and contains the evolutionary conserved insulin-family signature, as well as a reserved recognition site (Lys) in D domain, necessary to generate proteolytic cleavage for E-peptide. A significant structural difference was found in E domain in which flIGF-I possesses two potential alternative splicing donor site at $Val^{17,\;24}$ of E domain. Therefore, it seems so far that IGF-I sorely produces spliced variants due to the spliced E-peptide moiety while IGF-II appears to be maintained in a single type during evolution. IGF-II, however, may be also possible to transcribe unidentified variants, depending on the physiological conditions of tissues in vertebrates in vivo.

• Proceedings of the Korea Crystallographic Association Conference
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• 2002.11a
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• pp.25-25
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• 2002

CodWX, encoded by the cod operon in Bacillus subtilis, is a member of the ATP-dependent protease complex family, and is homologous to the eukaryotic 26S proteasome. It consists of two multimeric complexes: two hexameric ATPase caps of CodX and a protease chamber consisting of CodW dodecamer. Prior structural studies have shown that the N-terminal threonine residue is solely functional as a proteolytic nucleophile in ATP-dependent proteases such as HslV and certain β-type subunits of 20S proteasome, which have a primary sequence similarity of -50% and -20% with CodW respectively. Here we present a 3.0 Å resolution crystal structure of CodW, which is the first N-terminal serine protease among the known proteolytic enzymes. In spite of the same fold and the conserved contacts between subunits with HslV in E. coli and H. influenza, this structure shows the five additional residues extending from conserved Thr1 among the other ATP-dependent pretense and extraordinary basic proteolytic chamber.

• Mycobiology
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• v.29 no.3
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• pp.121-131
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• 2001

This study was carried out to identify the phylogenetic relationships among several caterpillar fungi by comparing the sequences of internal transcribed spacer regions(ITS1 and ITS2) and 5.8S ribosomal DNA(rDNA) repeat unit. The sequences of ITS1, ITS2, and the 5.8S rDNA from 10 strains of Cordyceps species, 12 strains of Paecilomyces, 3 strains of Beauveria, 2 strains of Metarhizium and 1 strains of Hirsutella were amplified, determined and compared with the previously known Cordyceps species. The sequences of 5.8S rDNA were more conserved in length and variation than those of ITS regions. Although the variable ITS sequences were often ambiguously aligned, the conserved sites could be found. In the phylogenetic tree, the species generally divided into three clusters, supported by their morphology and/or host ranges. The 5.8S rDNA and TTS1 sequences among 10 species of Cordyceps militaris were identical and only one base pair in ITS2 sequence was different. Cordyceps sinensis and Cordyceps ophioglossoides were also clearly different, although they belonged to the same cluster. The Geniank database search of species revealed sister taxa of an entomogenous fungus. Metarhizium was used as an putgroup in all taxa.

• Journal of Marine Bioscience and Biotechnology
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• v.2 no.4
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• pp.224-229
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• 2007

Muscle tissue expresses many muscle-specific genes, including myostatin (also known as GDF8) that is a member of the transforming growth factor-beta superfamily. Myostatin (MSTN) negatively regulates mammalian skeletal muscle growth and development by inhibiting myoblast proliferation. Mice and cattle possessing mutant MSTN alleles display a 'double muscling' phenotype characterized by extreme skeletal muscle hypertrophy and/or hyperplasia. In this study, we first have characterized partial cDNA of a MSTN gene from the muscle tissue in the F. chinensis and examined its expression pattern in various tissues. The partial MSTN gene (GenBank accession number EU 131093) in the F. chinensis was 1134 bp, encoding for 377 amino acids that showed 63-93% amino acid similarity to other vertebrate MSTNs, containing a conserved proteolytic cleavage site (RXRR) and conserved cysteine residues in the C-terminus. Based on a RT-PCR, the MSTN gene was expressed in the all tissues of F. chinensis used in this study.

• Molecules and Cells
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• v.19 no.1
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• pp.67-73
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• 2005

Isoflavones are synthesized by isoflavone synthases via the phenylpropanoid pathway in legumes. We have cloned two isoflavone synthase genes, IFS1 and IFS2, from a total of 18 soybean cultivars. The amino acid residues of the proteins that differed between cultivars were dispersed over the entire coding region. However, amino acid sequence variation did not occur in conserved domains such as the ERR triad region, except that one conserved amino acid was changed in the IFS2 protein of the GS12 cultivar ($R_{374}G$) and the IFS1 proteins of the 99M06 and Soja99s65 cultivars ($A_{109}T$, $F_{105}I$). In three cultivars (99M06, 99M116, and Simheukpi), most of amino acid changes were such that the difference between the amino acid sequences of IFS1 and IFS2 was reduced. The expression profiles of three enzymes that convert naringenin to the isoflavone, genistein, chalcone isomerase (CHI), isoflavone synthase (IFS) and flavanone 3-hydroxylase (F3H) were examined. In general, IFS mRNA was more abundant in etiolated seedlings than mature plants whereas the levels of CHI and F3H mRNAs were similar in the two stages. During seed development, IFS was expressed a little later than CHI and F3H but expression of these three genes was barely detectable, if at all, during later seed hardening. In addition, we found that the levels of CHI, F3H, and IFS mRNAs were under circadian control. We also showed that IFS was induced by wounding and by application of methyl jasmonate to etiolated soybean seedlings.

• Molecules and Cells
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• v.26 no.1
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• pp.41-47
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• 2008

Mitogen-activated protein kinase (MAPK) signaling is a crucial component of eukaryotic cells; it plays an important role in responses to extracelluar stimuli and in the regulation of various cellular activities. The signaling cascade is evolutionarily conserved in the eukaryotic kingdom from yeast to human. In response to a variety of extracellular signals, MAPK activity is known to be regulated via phosphorylation of a conserved $T{\times}Y$ motif at the activation loop in which both threonine and tyrosine residues are phosphorylated by the upstream kinase. However, the mechanism by which both residues are phosphorylated continues to remain elusive. In the budding yeast, Saccharomyces cerevisiae, Fus3 MAPK is involved in the mating signaling pathway. In order to elucidate the functional mechanism of MAPK activation, we quantitatively profiled phosphorylation of the $T{\times}Y$ motif in Fus3 using mass spectrometry (MS). We used synthetic heavy stable isotope-labeled phosphopeptides and nonphosphopeptides corresponding to the proteolytic $T{\times}Y$ motif of Fus3 and accompanying data-dependent tandem MS to quantitatively monitor dynamic changes in the phosphorylation events of MAPK. Phosphospecific immunoblotting and the MS data suggested that the tyrosine residue is dynamically phosphorylated upon stimulation and that this leads to dual phosphorylation. In contrast, the magnitude of threonine phosphorylation did not change significantly. However, the absence of a threonine residue leads to hyperphosphorylation of the tyrosine residue in the unstimulated condition, suggesting that the threonine residue contributes to the control of signaling noise.

• Molecules and Cells
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• v.26 no.1
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• pp.26-33
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• 2008

The plasmid pJB01, a member of the pMV158 family isolated from Enterococcus faecium JC1, contains three open reading frames, copA, repB, and repC. Plasmids included in this family produce counter-transcribed RNA (ctRNA) that contributes to copy number control. The pJB01 ctRNA, a transcript which consists of 54 nucleotides (nts), is encoded on the opposite strand from the copA/repB intergenic region and partially overlaps an atypical ribosome binding site (ARBS) for repB. The ARBS is integrated by the two underlined conserved regions: 5'-TTTTTGTNNNNTAANNNNNNNNNATG-3', and the ctRNA is complementary only to the 5' conserved sequence 5'-TTTTTGT-3'. This complementary sequence is located at a distance from the terminal loop of the ctRNA secondary structure. The ctRNA structure predicted by the mfold program suggests the possible generation of a terminal and an internal hairpin loop. The amount of in vitro translation product of repB mRNA was inversely proportional to the ctRNA concentration. Mutations in the terminal and internal hairpin loops of the ctRNA had inhibitory effects on its binding to the target mRNA. We propose that the intact structures of the terminal and internal hairpin loops, respectively, play important roles in forming the initial kissing and extending complexes between the ctRNA and target mRNA and that these regulate the copy number of this plasmid.

• Molecules and Cells
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• v.41 no.9
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• pp.842-852
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• 2018

Notch signaling is an evolutionarily conserved pathway and involves in the regulation of various cellular and developmental processes. Ligand binding releases the intracellular domain of Notch receptor (NICD), which interacts with DNA-bound CSL [CBF1/Su(H)/Lag-1] to activate transcription of target genes. In the absence of NICD binding, CSL down-regulates target gene expression through the recruitment of various corepressor proteins including SMRT/NCoR (silencing mediator of retinoid and thyroid receptors/nuclear receptor corepressor), SHARP (SMRT/HDAC1-associated repressor protein), and KyoT2. Structural and functional studies revealed the molecular basis of these interactions, in which NICD coactivator and corepressor proteins competitively bind to ${\beta}-trefoil$ domain (BTD) of CSL using a conserved ${\varphi}W{\varphi}P$ motif (${\varphi}$ denotes any hydrophobic residues). To date, there are conflicting ideas regarding the molecular mechanism of SMRT-mediated repression of CSL as to whether CSL-SMRT interaction is direct or indirect (via the bridge factor SHARP). To solve this issue, we mapped the CSL-binding region of SMRT and employed a 'one- plus two-hybrid system' to obtain CSL interaction-defective mutants for this region. We identified the CSL-interaction module of SMRT (CIMS; amino acid 1816-1846) as the molecular determinant of its direct interaction with CSL. Notably, CIMS contains a canonical ${\varphi}W{\varphi}P$ sequence (APIWRP, amino acids 1832-1837) and directly interacts with CSL-BTD in a mode similar to other BTD-binding corepressors. Finally, we showed that CSL-interaction motif, rather than SHARP-interaction motif, of SMRT is involved in transcriptional repression of NICD in a cell-based assay. These results strongly suggest that SMRT participates in CSL-mediated repression via direct binding to CSL.