• Korean Journal of Microbiology
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• v.55 no.2
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• pp.103-111
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• 2019

DNA methylation is involved in diverse processes in bacteria, including maintenance of genome integrity and regulation of gene expression. CcrM, the DNA methyltransferase conserved in Alphaproteobacterial species, carries out $N^6$-adenine or $N^4$-cytosine methyltransferase activities using S-adenosyl methionine as a co-substrate. Celeribacter marinus IMCC12053 from the Alphaproteobacterial group was isolated from a marine environment. Single molecule real-time sequencing method (SMRT) was used to detect the methylation patterns of C. marinus IMCC12053. Gibbs motif sampler program was used to observe the conversion of adenosine of 5'-GANTC-3' to $N^6$-methyladenosine and conversion of $N^4$-cytosine of 5'-GpC-3' to $N^4$-methylcytosine. Exocyclic DNA methyltransferase from the genome of strain IMCC12053 was chosen using phylogenetic analysis and $N^4$-cytosine methyltransferase was cloned. IPTG inducer was used to confirm the methylation activity of DNA methylase, and cloned into a pQE30 vector using dam-/dcm- E. coli as the expression host. The genomic DNA and the plasmid carrying methylase-encoding sequences were extracted and cleaved with restriction enzymes that were sensitive to methylation, to confirm the methylation activity. These methylases protected the restriction enzyme site once IPTG-induced methylases methylated the chromosome and plasmid, harboring the DNA methylase. In this study, cloned exocyclic DNA methylases were investigated for potential use as a novel type of GpC methylase for molecular biology and epigenetics.

• Journal of the Korean Society of Food Culture
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• v.34 no.2
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• pp.224-232
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• 2019

This study evaluated the physicochemical and microbial quality characteristic of seasonal commercial kimchi for hygienic safety levels. The pH of seasonal commercial kimchi was 3.84-6.36 and the titratable acidity and salinity of the samples were 0.21-1.16 and 1.19-1.54%, respectively. The content of nitrate and nitrite in the commercial kimchi were lower in the spring and summer, which was affected by acidic condition of the kimchi depending on fermentation. Heavy metal contents in commercial kimchi are not an issue because they were detected only at very low levels. The total aerobic bacteria and coliforms counts ranged from 5.25 to 8.44 Log CFU/g and 0.00 to 5.08 Log CFU/g, respectively. The total aerobic bacteria and coliforms were detected more in summer than in the other seasons. E. coli was detected in three of the samples tested. Food-borne pathogens were not detected in any of the samples except for B. cereus. B. cereus was detected in the fall in more than 70% of samples. These results suggest that commercial kimchi distributed in the fall maintain the quality properties and the microbiological safety of kimchi compared to the other seasons. Therefore, further studies as an effective distribution system for the particular seasons will be needed to guarantee the hygienic safety levels of commercial kimchi required by the consumers.

• Journal of Dairy Science and Biotechnology
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• v.36 no.4
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• pp.208-219
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• 2018

Emergence of drug resistant strains of Salmonella enterica threatens milk processing and related dairy industries, thereby increasing the need for development of new anti-bacterials. Developments of antibacterial drugs are largely aimed to target the bacterial envelope, but screening their efficacy on bacterial envelope is laborious. This study presents a potential biosensor for envelope-specific stress in which a gfp reporter gene fused to spy gene encoding a periplasmic chaperone protein Spy (spheroplast protein y) that can sense envelope stress signals transduced by two major two-component signal transduction systems BaeSR and CpxAR in Salmonella enterica serovars Enteritidis and S. Gallinarum. Using spy-gfp operon fusions in S. Enterititis and S. Gallinarum, we found that spy transcription in both serovars was greatly induced when Salmonella cells were forming the spheroplast and were treated with ethanol or a membrane-disrupting antibiotic polymyxin B. These envelope stress-specific inductions of spy transcription were abrogated in mutant Salmonella lacking either BaeR or CpxR. Results illustrate that induction of Spy expression can be efficiently triggered by two-component signal transduction systems sensing envelope stress conditions, and thereby suggest that monitoring the spy transcription by spy-gfp operon fusions would be helpful to determine if developing antimicrobials can damage envelopes of S. Enteritidis and S. Gallinarum.

• The Plant Pathology Journal
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• v.35 no.4
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• pp.351-361
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• 2019

In our previous study, pyrrolnitrin produced in Pseudomonas chlororaphis G05 plays more critical role in suppression of mycelial growth of some fungal pathogens that cause plant diseases in agriculture. Although some regulators for pyrrolnitrin biosynthesis were identified, the pyrrolnitrin regulation pathway was not fully constructed. During our screening novel regulator candidates, we obtained a white conjugant G05W02 while transposon mutagenesis was carried out between a fusion mutant $G05{\Delta}phz{\Delta}prn::lacZ$ and E. coli S17-1 (pUT/mini-Tn5Kan). By cloning and sequencing of the transposon-flanking DNA fragment, we found that a vfr gene in the conjugant G05W02 was disrupted with mini-Tn5Kan. In one other previous study on P. fluorescens, however, it was reported that the deletion of the vfr caused increased production of pyrrolnitrin and other antifungal metabolites. To confirm its regulatory function, we constructed the vfr-knockout mutant $G05{\Delta}vfr$ and $G05{\Delta}phz{\Delta}prn::lacZ{\Delta}vfr$. By quantifying ${\beta}-galactosidase$ activities, we found that deletion of the vfr decreased the prn operon expression dramatically. Meanwhile, by quantifying pyrrolnitrin production in the mutant $G05{\Delta}vfr$, we found that deficiency of the Vfr caused decreased pyrrolnitrin production. However, production of phenazine-1-carboxylic acid was same to that in the wild-type strain G05. Taken together, Vfr is required for pyrrolnitrin but not for phenazine-1-carboxylic acid biosynthesis in P. chlororaphis G05.

• Korean Journal of Agricultural Science
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• v.46 no.2
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• pp.351-359
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• 2019

The purpose of this study was to compare the growth performance, nutrient digestibility, fecal microflora, blood profiles and meat quality of broilers, Korean native chickens and white semi broilers under identical feeding conditions. Sixty 1-d chicks of each type were randomly placed into 12 pens per cage (5 chicks per cage) and fed commercial diets for 28, 49, and 28 days, respectively. The broilers showed a significantly higher (p < 0.05) growth performance from 0 to 4 weeks compared with the other types. Korean native chickens had a significantly higher (p < 0.05) digestibility of dry matter and nitrogen than that of the other species. The blood glucose was significantly higher in the Korean native chickens compared to the other species, and the blood cholesterol was significantly lower. The Lactobacillus content in Korean native chickens was significantly higher (p < 0.05) compared to the other species, and the E. coli content in the broilers was significantly higher (p < 0.05) than in the Korean native chickens and white semi broilers. In terms of meat quality, the breast meat of the broilers had a high water content and pH level. The breast meat of the white semi broilers had a significantly lower (p < 0.05) shear force than that of the other species. In conclusion, there was an interspecific physiological difference due to the age and body weight of the chickens. The broilers had a higher growth performance and meat quality compared to the Korean native chickens and white semi broilers.

• Journal of Microbiology and Biotechnology
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• v.32 no.2
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• pp.187-194
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• 2022

Two α-ʟ-arabinofuranosidases (BfdABF1 and BfdABF3) and a β-ᴅ-xylosidase (BfdXYL2) genes were cloned from Bifidobacterium dentium ATCC 27679, and functionally expressed in E. coli BL21(DE3). BfdABF1 showed the highest activity in 50 mM sodium acetate buffer at pH 5.0 and 25℃. This exo-enzyme could hydrolyze p-nitrophenyl arabinofuranoside, arabino-oligosaccharides (AOS), arabinoxylo-oligosaccharides (AXOS) such as 3²-α-ʟ-arabinofuranosyl-xylobiose (A³X), and 2³-α-ʟ-arabinofuranosyl-xylotriose (A²XX), whereas hardly hydrolyzed polymeric substrates such as debranched arabinan and arabinoxylans. BfdABF1 is a typical exo-ABF with the higher specific activity on the oligomeric substrates than the polymers. It prefers to α-(1,2)-ʟ-arabinofuranosidic linkages compared to α-(1,3)-linkages. Especially, BfdABF1 could slowly hydrolyze 2³,3³-di-α-ʟ-arabinofuranosyl-xylotriose (A²⁺³XX). Meanwhile, BfdABF3 showed the highest activity in sodium acetate at pH 6.0 and 50℃, and it has the exclusively high activities on AXOS such as A³X and A²XX. BfdABF3 mainly catalyzes the removal of ʟ-arabinose side chains from various AXOS. BfdXYL2 exhibited the highest activity in sodium citrate at pH 5.0 and 55℃, and it specifically hydrolyzed p-nitrophenyl xylopyranoside and xylo-oligosaccharides (XOS). Also, BfdXYL2 could slowly hydrolyze AOS and AXOS such as A³X. Based on the detailed hydrolytic modes of action of three exo-hydrolases (BfdABF1, BfdABF3, and BfdXYL2) from Bf. dentium, their probable roles in the hemiceullose-utilization system of Bf. dentium are proposed in the present study. These intracellular exo-hydrolases can synergistically produce ʟ-arabinose and ᴅ-xylose from various AOS, XOS, and AXOS.

• Microbiology and Biotechnology Letters
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• v.49 no.4
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• pp.534-542
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• 2021

Single-molecular guide RNA (sgRNA) plays a role in recognizing the DNA target sequence in CRISPR technology for genome editing and gene expression control. In this study, we systematically compared the length of the target recognition sequence in sgRNAs required for genome editing using Cas9-NG (an engineered Cas9 recognizing 5'-NG as PAM sequence) and gene expression control using deactivated Cas9-NG (dCas9-NG) by targeting the gal promoter in E. coli. In the case of genome editing, the truncation of three nucleotides in the target recognition sequence (TRS) of sgRNA was allowed. In gene expression regulation, we observed that target recognition and binding were possible even if eleven nucleotides were deleted from twenty nucleotides of the TRS. When 4 or more nucleotides are truncated in the TRS of the sgRNA, it is thought that the sgRNA/Cas9-NG complex can specifically bind to the target DNA sequence, but lacks endonuclease activity to perform genome editing. Our study will be helpful in the development of artificial transcription factors and various CRISPR technologies in the field of synthetic biology.

• Applied Chemistry for Engineering
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• v.33 no.4
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• pp.444-450
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• 2022

The effect of coated polyester (PET) textiles with metal oxide, chitosan, and copper ion on the antibacterial and antiviral activities was evaluated to investigate the applicability of multi-coated PET textiles as antiviral materials. Compared to coated PETs with a single agent, multi-coated PETs reduced the loading amount of coating materials as well as the contact time with bacteria for a bacterial cell number of < 10 CFU/mL, which was not detectable with the naked eyes. Metal oxides generate reactive oxygen species (ROS) such as free radicals by a catalytic reaction, and copper ions can promote contact killing by the generation of ROS. Chitosan not only enhanced antibacterial activities due to amine groups, but enabled it to be a template to load copper ions. We observed that multi-coated PET textiles have both antibacterial activities for E. coli and S. aureus and antiviral efficiency of more than 99.9% for influenza A (H1N1) and SARS-CoV-2. The multi-coated PET textiles could also be prepared via a roll-to-roll coating process, which showed high antiviral efficacy, demonstrating its potential use in air filtration and antiviral products such as masks and personal protective equipment.

• Journal of Animal Science and Technology
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• v.64 no.1
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• pp.23-37
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• 2022

Thirty-six weaned piglets with an initial body weight (BW) of 8.43 ± 0.40 kg (28 days of age, ([Landrace × Yorkshire] × Duroc) were randomly assigned to 6 treatments for a 2-week feeding trial to determine the effects of different inorganic zinc (IZ), organic zinc (OZ) or combination of low crude protein diet (LP) and Mixed feed additive (MFA) on diarrhea score, nutrient digestibility, zinc utilization, blood profiles, organ weight, and fecal microflora in weaned piglet diet. The pigs were individually placed in 45 × 55 × 45 cm stainless steel metabolism cages in an environmentally controlled room (30 ± 1℃). The dietary treatments included a negative control (NC), positive control (PC; zinc oxide, 1,000 mg/kg), T1 (IZ : OZ, 850 : 150), T2 (IZ : OZ 700 : 300), T3 (IZ : OZ, 500 : 500), and T4 (LP + MFA [0.1% Essential oils + 0.08% Protease + 0.02% Xylanase]). The daily feed allowance was adjusted to 2.7 times the maintenance requirement for digestible energy (2.7 × 110 kcal of DE/kg BW^0.75). This allowance was divided into two equal parts, and the piglets were fed at 08 : 30 and 17 : 30 each day. Water was provided ad libitum through a drinking nipple. The diarrhea score was significantly increased (p < 0.05) in NC treatment compared with other treatments. The apparent total tract digestibility (ATTD) of dry matter (DM), nitrogen (N), and gross energy (GE) was significantly increased (p < 0.05) in the T2 treatment compared with the PC and NC treatments in week 1. In week 2, the ATTD of DM, N, and GE was significantly decreased (p < 0.05) in the NC treatment compared with other treatments. The T3 treatment had significantly higher (p < 0.05) ATTD and apparent ileal digestibility of zinc than the PC and T1 treatments. The Escherichia coli count in feces was significantly decreased in the T4 treatment compared with the NC and T2 treatments. The Lactobacillus count in feces was significantly increased in the T4 and T1 treatment compared with the T2 and T3 treatments. In conclusion, IZ : OZ 500 : 500 levels could improve nutrient digestibility and zinc utilization in weaned piglets, Moreover, MFA in LP diets could be used as a zinc alternative.

• Journal of Life Science
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• v.32 no.12
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• pp.997-1004
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• 2022

To verify the nutritional superiority and safety of Protaetia brevitarsis larvae fed a food source containing soybean curd cake, the nutrients and harmful substances of larvae reared only with fermented oak sawdust and a food source containing soybean curd cake were comparatively analyzed. The crude protein content was 50.0% in the larvae fed with a food source containing soybean curd cake (SCC), which was 1.1 times higher than that of the larvae fed with fermented oak sawdust (FOS) at 44.7%. Potassium, which showed the highest content among macrominerals, was 2.5 times higher in SCC (3,169.6 mg/100 g) than in FOS (1,245.9 mg/100 g). Among trace minerals, zinc showed 12.6 times higher content than FOS (8.2 mg/100 g) in SCC (103.0 mg/100 g). As a result of the analysis of harmful substances, all heavy metals met the edible insect control standards, and pathogenic microorganisms, such as E. coli and Salmonella spp, were not detected. According to the above study, the larvae of P. brevitarsis fed soybean curd cake contain various nutrients, and safety has also been confirmed, so it is judged to be suitable for use as food.