• Journal of the Korean Magnetic Resonance Society
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• v.25 no.3
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• pp.39-44
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• 2021

The CRISPR-Cas system provides adaptive immunity for bacteria and archaea against invading phages and foreign plasmids. In the Class 1 CRISPR-Cas system, multi-subunit Cas proteins assemble with crRNA to bind to DNA targets. To disarm the bacterial defense system, bacteriophages evolved anti-CRISPR (Acr) proteins that actively inhibit the host CRISPR-Cas function. Here we report the backbone resonance assignments of AcrIF7 protein that inhibits the type I-F CRISPR-Cas system of Pseudomonas aeruginosa using triple-resonance nuclear magnetic resonance spectroscopy. We employed various computational methods to predict the structure and binding interface of AcrIF7, and assessed the model with experimental data. AcrIF7 binds to Cas8f protein via flexible loop regions to inhibit target DNA binding, suggesting that conformational heterogeneity is important for the Cas-Acr interaction.

• Proceedings of the Zoological Society Korea Conference
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• 2002.04a
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• pp.25-32
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• 2002

No Abstract, See Full Text

• Biomolecules & Therapeutics
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• v.3 no.4
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• pp.311-315
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• 1995

The K. aerogenes ureal gene product was previously shown to facilitate assembly of the crease metallocenter (Lee, M. H., Mulrooney, S. B., Renner, M. J., Markowicz, Y., and Hausinger, R. P. (1992) J. Bacteriol. 174, 4324-4330). UreG protein has now been purified and characterized. Although the protein is predicted to possess a putative NTP-binding P-loop motif, equilibrium dialysis studies showed negative results. Immunogold electron microscopic studies using polyclonal antibodies directed against UreG protein confirm that UreG is located in the cytoplasm as predicted in the DNA sequence.

• Journal of the Korean Magnetic Resonance Society
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• v.16 no.1
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• pp.22-33
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• 2012

Tid1, belonging to the Hsp40/DnaJ family of proteins, functions as a cochaperone of cytosolic and mitochondrial Hsp70 proteins. In particular, the N-terminal J-domain of Tid1 (Tid1-JD) constitutes the major binding sites for proteinprotein interactions with client proteins, including p53, as well as its partner chaperone, Hsp70. In the present study, soluble, recombinant protein of Tid1-JD could be obtained by using the pCold vector system, and backbone NMR assignments were completed using the isotope $[^{13}C/^{15}N]$-enriched protein. Far-UV CD result implied that Tid1-JD is an ${\alpha}$-helical protein and the secondary structure determined using chemical shift data sets indentified four ${\alpha}$-helices with a loop region containing the HPD (conserved tripeptide of His, Pro and Asp) motif. Additionally, NMR spectra under different conditions implied that the HPD motif, which is a critical region for protein-protein interactions of Tid1-JD, would possess dynamic properties.

• Korean Journal of Microbiology
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• v.47 no.2
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• pp.103-109
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• 2011

Pectobacterium carotovorum subsp. carotovorum is the causative agent of soft rot in crops such as potato and cabbages. Loop-mediated isothermal amplification (LAMP) is a simple DNA amplification method, as well as isothermal PCR technique. In this study, a new method for the rapid detection of Pectobacterium carotovorum subsp. carotovorum was developed using LAMP that named PCC-LAMP. Based on lytic murein transglycolase gene of Pectobacterium carotovorum subsp. carotovorum, a set of four primers for LAMP was designed. The optimal PCC-LAMP reaction temperature was established at $61^{\circ}C$. Under standard conditions, PCC-LAMP amplified $1{\times}10^3$ copies of clone PCC-pBX437 per reaction. Further, this method can also assay directly by SYBR Green I without electrophoresis. Amplification was not detected for five other bacterial species. In conclusion, PCC-LAMP may be a useful method for the detection Pectobacterium carotovorum subsp. carotovorum in the field.

• Microbiology and Biotechnology Letters
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• v.44 no.4
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• pp.493-496
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• 2016

Peach rosette mosaic virus (PRMV) is a plant virus that was first reported in 1933 by Peach. It can infect hosts including peach, grape, blueberry, dandelion, plum, cherry tree, and weeds. PRMV is non-reportable in Korea, but it is designated as a controlled virus requiring plant quarantine. In this study, for the rapid and specific detection of PRMV, we developed an assay using loop-mediated isothermal amplification (LAMP). Comparison between conventional polymerase chain reaction (PCR) methods (real time-PCR and nested PCR) and LAMP for the detection of PRMV revealed an equivalent level of sensitivity by all the tested methods. For the LAMP assay, outer primer sets were used to amplify a 264-bp PCR product, which was then digested using the restriction enzyme Pvu II (CAG/CTG), and the visualization of two digestion fragments (207 + 57 bp) indicated a positive reaction. The developed LAMP assay for PRMV is expected to enable the rapid monitoring of PRMV in plants.

• Korean Journal of Poultry Science
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• v.39 no.4
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• pp.311-315
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• 2012

The increasing demand for Korean native chicken meat indicates that the discovery of haplotypes is very important from both economic and conservation points of view. In this study, mtDNA D-loop sequences from two crossbred Korean native chicken populations of 138 individuals were investigated. Twenty six nucleotide substitutions were identified from sequence analysis and were classified into 12 haplotypes. The haplotype H_8 represents 73.47% of Woorimatdag (chicken population) sequences, which were identified in all five Woorimatdag chicken populations investigated. The H_7 haplotype (Dhap1) for D population covers 45% sequences, which indicate maternal inheritance from black Korean native chicken. On the other hand, Chap3 and Chap4 for C population are specific haplotypes, as H_5 and H_2, respectively. Based on the network profiles, six SNPs (C199T, A239G, G242A, A291G, T330C and C391A) of the D-loop region are effective markers for discrimination between Woorimatdag and Hanhyup chicken populations. Also, the phylogenetic analyses of Woorimatdag and Hanhyup chicken populations were used to identify the genetic relationships among the haplotypes. The results presented here can be used for developing molecular markers to discriminate between two commercial Korean native chickens.

• Food Science of Animal Resources
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• v.37 no.3
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• pp.464-468
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• 2017

The identification of pork in commercially processed meats is one of the most crucial issues in the food industry because of religious food ethics, medical purposes, and intentional adulteration to decrease production cost. This study therefore aimed to develop a method for the detection of pork adulteration in meat products using primers specific for pig mitochondrial DNA. Mitochondrial DNA sequences for pig, cattle, chicken, and sheep were obtained from GenBank and aligned. The 294-bp mitochondrial DNA D-loop region was selected as the pig target DNA sequence and appropriate primers were designed using the MUSCLE program. To evaluate primer sensitivity, pork-beef-chicken mixtures were prepared as follows: i) 0% pork-50% beef-50% chicken, ii) 1% pork-49.5% beef-49.5% chicken, iii) 2% pork-49% beef-49% chicken, iv) 5% pork-47.5% beef-47.5% chicken, v) 10% pork-45% beef-45% chicken, and vi) 100% pork-0% beef-0% chicken. In addition, a total of 35 commercially packaged products, including patties, nuggets, meatballs, and sausages containing processed chicken, beef, or a mixture of various meats, were purchased from commercial markets. The primers developed in our study were able to detect as little as 1% pork in the heat treated pork-beef-chicken mixtures. Of the 35 processed products, three samples were pork positive despite being labeled as beef or chicken only or as a beef-chicken mix. These results indicate that the developed primers could be used to detect pork adulteration in various processed meat products for application in safeguarding religious food ethics, detecting allergens, and preventing food adulteration.

• International Journal of Industrial Entomology and Biomaterials
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• v.9 no.2
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• pp.187-191
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• 2004

Actin is a ubiquitous and highly conserved protein found in eukaryotic organisms. In this study, we describe the cDNA cloning and mRNA expression of an actin gene from the mulberry longicorn beetle, Apriona germari. The A. germari actin cDNA is 1524 bp containing a complete 1128 bp open reading frame that encodes a polypeptide of 376 amino acid residues with a predicted molecular weight of about 41.5 kDa. The deduced amino acid sequence of the A.germari actin cDNA showed 99% protein sequence identity to Homalodisca coagulata actin, differing at only two amino acid positions, and 92-98% protein sequence identity to known insect species actins. The predicted three-dimensional structure of A. germari actin revealed the four residue hydrophobic pulg loop characteristic of the actin family. Northern blot analysis showed that A. germari actin is highly expressed in epidermis and muscle, and less strongly in midgut, but not in the fat body of A. germari larva.

• Genomics & Informatics
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• v.21 no.3
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• pp.39.1-39.15
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• 2023

DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intraspecific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.