• Journal of Life Science
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• v.11 no.2
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• pp.111-115
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• 2001

This study was designed to clone the SNF2/SW12 helicase-related genes from the fission yeast Schizosaccha-romyces pombe and thereafter to elucidate the common functions of the proteins in this family. The $hrp^{2+}$gene was cloned by polymerase chain reaction amplification using degenerative primers from conserved SNF2 motifs within the ERCC6 gene, which encodes a protein involved in DNA excision repair. Like other SNF2/SW12 family proteins, the deduced amino acid sequence of Hrp2 contains DNA-dependent ATPase/7 helicase domains as well as the chromodomain and the DNA binding domain. This configuration is similar to that of mCHD1 (mouse chromo-ATPase/helicase-DNA-dinding protein 1), suggesting that Hrp2 is a S. pombe homolog of mCHD1, which is thought to function in altering the chromatin structure to control the gene expression. To characterize the function of Hrp2, 4 Uracil-Hrp2 fusion protein, it was purified near homogeneity by affinity chromatography on $Ni^{2+}$-NTA agarose, DEAE-Sepharose ion exchange arid Sephacryl S-200 gel filtration chromatographies. The purified fusion protein exhibited DNA-dependent ATPase activity, which was stimulated by both double-stranded and single-stranded DNA. To determine the steady-state level of $hrp^{2+}$ transcripts during growth, cells were cultured in medium and collected at every 2hr to prepare total RNAs. The northern blot analysis showed that the level of $hrp^{2+}$ transcripts reached its maximum before the cells entered the exponential growth phase and then decreased gradually, This result implies that Hrp2 may be required at early stages of cell growth.h.

• Journal of Marine Life Science
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• v.8 no.2
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• pp.104-114
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• 2023

As plastic usage increases globally, the amount of plastic waste entering the marine environment is steadily rising. Microplastics, in particular, can be ingested by marine organisms and accumulated in their digestive tracts, causing harmful effects on their growth and reproduction. Cytochrome P450 (CYP) enzymes are known to metabolize various environmental pollutants as detoxification enzymes, but their role in crustaceans is not well understood. In this study, sequences of nine CYP genes (CYP370A4, CYP370C5 from clan 2; CYP350A1, CYP350C5, CYP361A1 from clan 3; CYP4AN-like, CYP4AP2, CYP4AP3, CYP4C33-like1 from clan 4) were analyzed using conserved domains in the brackish water flea Diaphanosoma celebensis. Additionally, after exposure to three different sizes of polystyrene beads (0.05-, 0.5-, 6-㎛ PS beads; 0.1, 1, and 10 mg/L) for 48 hours, the expression of these nine CYP genes were investigated using real-time reverse transcription polymerase chain reaction (RT-PCR). The results showed that all CYP genes possessed conserved motifs, indicating that D. celebensis CYP has evolutionarily conserved functions. Among these CYP genes, the expression of CYP370C5, CYP360A1, and CYP4C122 showed a significant increase after exposure to 0.05-㎛ PS beads, suggesting their involvement in PS metabolism. This research will contribute to understanding the molecular mode of actions of microplastics on marine invertebrates.

• BMB Reports
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• v.34 no.1
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• pp.73-79
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• 2001

Transcriptional activation domains are known to be inherently "unstructured" with no tertiary structure. A recent NMR study, however, has shown that the transactivation domain in human p53 is populated with an amphipathic helix and two nascent turns. This suggests that the presence of such local secondary structures within the overall "unstructured" structural framework is a general feature of acidic transactivation domains. These pre-existing local structures in p53, formed selectively by positional conserved hydrophobic residues that are known to be critical for transcriptional activity, thus appear to constitute the specific structural motifs that regulate recognition of the p53 transactivation domain by target proteins. Here, we report the results of a NMR structural comparison between the native human p53 transactivation domain and an inactive mutant (22L,23W$\rightarrow$22R,23S). Results show that the mutant has an identical overall structural topology as the native protein, to the extent that the amphipathic helix formed by the residues 18T 26L within the native p53 transactivating domain is preserved in the double mutant. Therefore, the lack of transcriptional activity in the double mutant should be ascribed to the disruption of the essential hydrophobic contacts between the p53 transactivation domain and target proteins due to the (22L,23W$\rightarrow$22R,23S) mutation.

• Korean Journal of Ichthyology
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• v.23 no.1
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• pp.61-69
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• 2011

Gene and promoter structures of metallothionein(MT) from Miho spine loach (Cobitis choii; Cypriniformes) were characterized, and the transcriptional responses to experimental exposures to heavy metals and heat stress were examined. The C. choii metallothionein displayed well-conserved features of teleostean metallothioneins at gDNA, mRNA and amino acid levels. Bioinformatic analysis predicted that the C. choii MT regulatory region potentially possessed various motifs or elements targeted by various transcription factors associated with metal-coordinating regulation (e.g., metal transcription factor-1), immune responses (e.g., nuclear factor kappa B), and thermal modulations (e.g., heat shock factor). Acute heavy-metal exposures to 0.5 or $1.0\;{\mu}M$ of cadmium (Cd), copper (Cu), manganese (Mn), nickel (Ni) or zinc (Zn) showed that MT transcription was significantly stimulated by Cd (9.6-fold relative to non-exposed control) and Cu (10.4-fold), only moderately by Mn (2.4-fold), but hardly by Ni and Zn. Elevation of water temperature from $25^{\circ}C$ to $31^{\circ}C$ caused a rapid modulation of MT mRNAs toward upregulation to 9.5-fold; however, afterward the elevated mRNA level slightly decreased during further incubation at $31^{\circ}C$ for 6 h. Results from this study suggest that MT-based expression assay could be a useful basis for better understanding the metal- and/or heat-caused stresses in this endangered fish species.

• Parasites, Hosts and Diseases
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• v.48 no.4
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• pp.319-324
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• 2010

A family of calcium-dependent protein kinases (CDPKs) is a unique enzyme which plays crucial roles in intracellular calcium signaling in plants, algae, and protozoa. CDPKs of malaria parasites are known to be key regulators for stage-specific cellular responses to calcium, a widespread secondary messenger that controls the progression of the parasite. In our study, we identified a gene encoding Plasmodium vivax CDPK4 (PvCDPK4) and characterized its molecular property and cellular localization. PvCDPK4 was a typical CDPK which had well-conserved N-terminal kinase domain and C-terminal calmodulin-like structure with 4-EF hand motifs for calcium-binding. The recombinant protein of EF hand domain of PvCDPK4 was expressed in Echerichia coli and a 34 kDa product was obtained. Immunofluorescence assay by confocal laser microscopy revealed that the protein was expressed at the mature schizont of P. vivax. The expression of PvCDPK4-EF in schizont suggests that it may participate in the proliferation or egress process in the life cycle of this parasite.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.59 no.3
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• pp.263-281
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• 2014

Transcription factors are essential for the regulation of gene expression in plant. They are binding to either enhancer or promoter region of DNA adjacent to the gene and are related to basal transcription regulation, differential enhancement of transcription, development, response to intercellular signals or environment, and cell cycle control. The mechanism in controlling gene expression of transcription can be understood through the assessment of the complete sequence for the maize genome. It is possible that the maize genome encodes 4,000 or more transcription factors because it has undergone whole duplication in the past. Previously, several transcription factors of maize have been characterized. In this review article, the transcription factors were selected using Pfam database, including many family members in comparison with other family and listed as follows: ABI3/VP1, AP2/EREBP, ARF, ARID, AS2, AUX/IAA, BES1, bHLH, bZIP, C2C2-CO-like, C2C2-Dof, C2C2-GATA, C2C2-YABBY, C2H2, E2F/DP, FHA, GARP-ARR-B, GeBP, GRAS, HMG, HSF, MADS, MYB, MYB-related, NAC, PHD, and WRKY family. For analyzing motifs, each amino acid sequence has been aligned with ClustalW and the conserved sequence was shown by sequence logo. This review article will contribute to further study of molecular biological analysis and breeding using the transcription factor of maize as a strategy for selecting target gene.

• Journal of Life Science
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• v.14 no.1
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• pp.38-44
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• 2004

Two genes, SinIFS1 and SinIFS2 from Korean soybean cultivar, Sinpaldalkong known as one of isoflavonerich cultivars, were cloned with PCR and degenerate primers. The sequences of two genes were analyzed with previously reported IFS genes of leguminous plants and their expression pattern in various environmental conditions was surveyed. The genomic clone of SinIFS1 contained 1,828bp nucleotides and encoded a polypeptide of 521 amino acids, and 1912bp nucleotides and a polypeptide of 521 amino acids for SinIFS2. Both genes included several conserved motifs, oxygen binding and activation (A/G-G-X-E/D-T-T/S), ERR triad (E...R....R), and heme binding (F-X-X-G-X-R-X-C-X-G) domain, which are typical in any member of cytochrome P45O superfamily. Very high sequence homology (>98%) was observed in the comparison with other IFSs of legumes. In the northern blot analysis to check the expression and increase of SinIFS1 to various environmental renditions (low temperature, light, dark, UV, and fungal elicitor), the most significant induction, more than 6 times of transcript level compared to the dark treatment as a control, was observed from the fungal elicitor treatment. The next up-regulated expression was from UV treatment (4${\times}$), low temperature and light conditions.

• Proceedings of the Korean Society of Applied Pharmacology
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• 2002.07a
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• pp.113-113
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• 2002

Phylogenetically conserved Bcl-2 family proteins play a pivotal role in the regulation of apoptosis from virus to human. Members of the Bcl-2 family consist of antiapoptotic proteins such as Bcl-2, Bcl-xL, and Bcl-w, and proapoptotic proteins such as BAD, Bax, BOD, and Bok. It has been proposed that anti- and proapoptotic Bcl-2 proteins regulate cell death by binding to each other and forming heterodimers. A delicate balance between anti- and proapoptotic Bcl-2 family members exists in each cell and the relative concentration of these two groups of proteins determines whether the cell survives or undergoes apoptosis. Mcl-1 (Myeloid cell :leukemia-1) is a member of the Bcl-2 family proteins and was originally cloned as a differentiation-induced early gene that was activated in the human myeloblastic leukemia cell line, ML-1 . Mcl-1 is expressed in a wide variety of tissues and cells including neoplastic ones. We recently identified a short splicing variant of Mcl-1 short (Mcl-IS) and designated the known Mcl-1 as Mcl-1 long (Mcl-lL). Mcl-lL protein exhibits antiapoptotic activity and possesses the BH (Bcl-2 homology) 1, BH2, BH3, and transmembrane (TM) domains found in related Bcl-2 proteins. In contrast, Mcl-1 S is a BH3 domain-only proapoptotic protein that heterodimerizes with Mcl-lL. Although both Mc1-lL and Mcl-lS proteins contain BH domains fecund in other Bcl-2 family proteins, they are distinguished by their unusually long N-terminal sequences containing PEST (proline, glutamic acid, serine, and threonine) motifs, four pairs of arginine residues, and alanine- and glycine-rich regions. In addition, the expression pattern of Mcl-1 protein is different from that of Bcl-2 suggesting a unique role (or Mcl-1 in apoptosis regulation. Tankyrasel (TRF1-interacting, ankyrin-related ADP-related polymerasel) was originally isolated based on its binding to TRF 1 (telomeric repeat binding factor-1) and contains the sterile alpha motif (SAM) module, 24 ankyrin (ANK) repeats, and the catalytic domain of poly(adenosine diphosphate-ribose) polymerase (PARP). Previous studies showed that tankyrasel promotes telomere elongation in human cells presumably by inhibiting TRFI though its poly(ADP-ribosyl)action by tankyrasel . In addition, tankyrasel poly(ADP-ribosyl)ates Insulin-responsive amino peptidase (IRAP), a resident protein of GLUT4 vesicles, and insulin stimulates the PARP activity of tankyrase1 through its phosphorylation by mitogen-activated protein kinase (MAPK). ADP-ribosylation is a posttranslational modification that usually results in a loss of protein activity presumably by enhancing protein turnover. However, little information is available regarding the physiological function(s) of tankyrase1 other than as a PARP enzyme. In the present study, we found tankyrasel as a specific-binding protein of Mcl-1 Overexpression of tankyrasel led to the inhibition of both the apoptotic activity of Mel-lS and the survival action of Mcl-lL in mammalian cells. Unlike other known tankyrasel-interacting proteins, tankyrasel did not poly(ADP-ribosyl)ate either of the Mcl-1 proteins despite its ability to decrease Mcl-1 proteins expression following coexpression. Therefore, this study provides a novel mechanism to regulate Mcl-1-modulated apoptosis in which tankyrasel downregulates the expression of Mcl-1 proteins without the involvement of its ADP-ribosylation activity.

• Journal of Microbiology and Biotechnology
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• v.20 no.12
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• pp.1735-1743
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• 2010

The full-length genes gyrB (2,415 bp), parC (2,277 bp), and parE (1,896 bp) in Edwardsiella tarda were cloned by PCR with degenerate primers based on the sequence of the respective quinolone resistance-determining region (QRDR), followed by elongation of 5' and 3' ends using cassette ligation-mediated PCR (CLMP). Analysis of the cloned genes revealed open reading frames (ORFs) encoding proteins of 804 (GyrB), 758 (ParC), and 631 (ParE) amino acids with conserved gyrase/topoisomerase features and motifs important for enzymatic function. The ORFs were preceded by putative promoters, ribosome binding sites, and inverted repeats with the potential to form cruciform structures for binding of DNA-binding proteins. When comparing the deduced amino acid sequences of E. tarda GyrB, ParC, and ParE with those of the corresponding proteins in other bacteria, they were found to be most closely related to Escherichia coli GyrB (87.6% identity), Klebsiella pneumoniae ParC (78.8% identity), and Salmonella Typhimurium ParE (89.5% identity), respectively. The two topoisomerase genes, parC and parE, were found to be contiguous on the E. tarda chromosome. All 18 quinolone-resistant isolates obtained from Korea thus far did not contain subunit alternations apart from a substitution in GyrA (Ser83$\rightarrow$Arg). However, an alteration in the QRDR of ParC (Ser84$\rightarrow$Ile) following an amino acid substitution in GyrA (Asp87$\rightarrow$Gly) was detected in E. tarda mutants selected in vitro at $8{\mu}g/ml$ ciprofloxacin (CIP). A mutant with a GyrB (Ser464$\rightarrow$Leu) and GyrA (Asp87$\rightarrow$Gly) substitution did not show a significant increase in the minimum inhibitory concentration (MIC) of CIP. None of the in vitro mutants exhibited mutations in parE. Thus, gyrA and parC should be considered to be the primary and secondary targets, respectively, of quinolones in E. tarda.

• Parasites, Hosts and Diseases
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• v.57 no.6
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• pp.671-680
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• 2019

Cathepsin D (CatD, EC 3.4.23.5) is a member belonging to the subfamily of aspartic endopeptidases, which are classified into the MEROPS clan AA, family A1. Helminth parasites express a large set of different peptidases that play pivotal roles in parasite biology and pathophysiology. However, CatD is less well known than the other classes of peptidases in terms of biochemical properties and biological functions. In this study, we identified 2 novel CatDs (CsCatD1 and CsCatD2) of Clonorchis sinensis and partially characterized their properties. Both CsCatDs represent typical enzymes sharing amino acid residues and motifs that are tightly conserved in the CatD superfamily of proteins. Both CsCatDs showed similar patterns of expression in different developmental stages of C. sinensis, but CsCatD2 was also expressed in metacercariae. CsCatD2 was mainly expressed in the intestines and eggs of C. sinensis. Sera obtained from rats experimentally infected with C. sinensis reacted with recombinant CsCatD2 beginning 2 weeks after infection and the antibody titers were gradually increased by maturation of the parasite. Structural analysis of CsCatD2 revealed a bilobed enzyme structure consisting of 2 antiparallel β-sheet domains packed against each other forming a homodimeric structure. These results suggested a plausible biological role of CsCatD2 in the nutrition and reproduction of parasite and its potential utility as a serodiagnostic antigen in clonorchiasis.