• Journal of Animal Science and Technology
• /
• v.49 no.6
• /
• pp.719-728
• /
• 2007

The cysteine and glycine rich protein 3 (CSRP3), apolipoprotein B mRNA editing enzyme catalytic polypeptide‐like 2(APOBEC2) and caveolin (CAV) gene family(CAV1, CAV2, CAV3) have been reported to play important roles for carcass and meat quality traits in pig, mouse, human and cattle. As an initial step, we investigated SNPs in these 5 genes among eight different cattle breeds. Eighteen primer pairs were designed from bovine sequence data of NCBI database to amplify the partial gene fragments. Sequencing results revealed 9 SNPs in the coding regions of three caveolin genes, 1 SNP in CSRP3 and 3 SNPs in APOBEC2 gene. All the identified SNPs were confirmed by PCR-RFLP. Also, 9 more intronic SNPs were detected in these genes. However, all identified mutations in the coding region do not change amino acid sequence. Allelic distributions were significantly different for 5 SNPs in CAV2, CAV3, CSRP3 and APOBEC2 genes among the eight different breeds. These results gave some clues about the polymorphisms of these genes among the cattle breeds and will be useful for further searches for identifying association between these SNPs and meat quality traits in cattle.

• The Journal of Korean Society of Virology
• /
• v.29 no.4
• /
• pp.247-259
• /
• 1999

Small round structured viruses (SRSV) are the major ethological agents which can cause outbreaks of non-bacterial gastroenteritis or food poisoning both in children and adults. The classification of family Caliciviridae to which SRSV belong, is based on the genome encoding three open reading frames. The rotavirus is another major pathogen which causes diarrhea in young children. We examined stool specimens obtained from diarrheal patients in Wonju from which bacterial pathogens were not found. To detect causative viruses from stool specimens of patients, reverse transcription (RT)-polymerase chain reaction (PCR) or nested PCR using rotavirus or SRSV specific primers was performed. In this study, RT-nested PCR procedure which can amplify a 330 bp fragment derived from RNA dependent RNA polymerase (RDRP) region within ORF1 was applied for the detection of SRSV. For the detection of rotaviruses, a 877 bp fragment from the VP4 region of rotavirus genome was amplified. As a result, rotavirus was not detected while SRSV sequences were detected from one out of five specimens. The nucleotide and amino acid sequences of the Wonju isolate were compared with other 6 Korean isolates which have been isolated and sequenced in our laboratory. Sequence analysis revealed that the Wonju isolate was rather distinct from other Korean isolates: the Wonju isolate was closer to genogroup I of SRSV while other 6 Korean isolates belonged to genogroup II.

• Applied Biological Chemistry
• /
• v.41 no.2
• /
• pp.125-129
• /
• 1998

Xanthomonas sp. isolated from soil exhibited cell wall lytic activity of Candida albicans and secreted chitinase in chitin media. Especially, the chitinase activity was induced by chitin and reached a maximum level at 3 days culture in chitin media. We constructed genomic library of Xanthomonas sp. using cosmid vector in E. coli. Oligonucleotide probe was synthesized from the consensus sequence corresponding to chitinase active site, which was derived from the comparison of amino acid sequences of bacterial chitinase genes. Using this oligonucleotide probe, we screened the genomic library. By restriction enzyme mapping of the positive clones, we identified 4 independent clones which may contain the chitinase gene. One of the clones, named pXCH1 (1.2 kb insert), was further analyzed. Northern blot analysis indicated that is transcripts, 1 kb and 0.8 kb, were induced by chitin. When the cloned gene was induced by IPTG in E.coli cell, chitinase activity which was secreted onto culture media was not observed. However, when the cell was disrupted by using sonicator and then centrifuged, the supernatant exhibited chitinase activity. SDS-PAGE of the supernatant indicated that about 35 kDa protein was induced by IPTG. From these results, it was concluded that the cloned DNA was one of the chitinase genes of Xanthomonas sp.

• Korean Journal of Microbiology
• /
• v.38 no.2
• /
• pp.67-73
• /
• 2002

The cellular responses of soil-borne bacterium, Pseudomonas sp. HK-6 to explosive 2,4,6-trinitrotoluene (TNT) were examined. Two stress shock proteins (SSPs), approximately 70-kDa DnaK and a 60-kDa GroEL were found in HK-6 cells in response to TNT. Analyses of SDS-PAGE and Western blot using anti-DnaK and GroEL revealed that SSPs were induced in HK-6 cells exposed to 0.5 M of TNT far 6-12 hrs. The maximum induction of proteins was achieved at 8-hr incubation point after HK-6 cells'exposure to TNT. Similar SSPs were found to be induced in HK-6 cells by heat shock (shift of temperature, from $30^{\circ}C$ to $42^{\circ}C$) or cold shock (shift of temperature,$30^{\circ}C$ to $4^{\circ}C$).2D-PAGE of soluble protein tractions from the culture of Pseudomonas sp. HX-6 exposed to TNT demonstrated that approximately 450 spots were observed on the silver stained gels ranging from pH 3 to pH 10. Among them, 12 spots significantly induced and expressed in response to TNT were selected and analyzed. Approximately 60-kDa protein, which was assumed highly expressed on the gel, was used for amino acid sequencing. N-terminal microsequencing with in-gel digestion showed that N-terminal sequence of the TNT-induced protein, <$^1XXAKDVKFGDSARKKML^17$, shared extensive similarity with $^1XXAKDVKFGDSARKKML^17$, N-terminal sequence of (P48216) GroEL of Pseudomonas putida.

• Journal of Microbiology
• /
• v.44 no.2
• /
• pp.192-199
• /
• 2006

Pseudomonas putida KL47 is a natural isolate that assimilates benzene, 1-alkylbenzene $(C_1-C_4)$, biphenyl, p-cumate, and p-cymene. The genetic background of strain KL47 underlying the broad range of growth substrates was examined. It was found that the cym and cmt operons are constitutively expressed due to a lack of the cymR gene, and the tod operon is still inducible by toluene and biphenyl. The entire array of gene clusters responsible for the catabolism of toluene and p-cymene/p-cumate has been cloned in a cosmid vector, pLAFR3, and were named pEK6 and pEK27, respectively. The two inserts overlap one another and the nucleotide sequence (42,505 bp) comprising the cym, cmt, and tod operons and its flanking genes in KL47 are almost identical (>99 %) to those of P. putida F1. In the cloned DNA fragment, two genes with unknown functions, labeled cymZ and cmtR, were newly identified and show high sequence homology to dienelactone hydrolase and CymR proteins, respectively. The cmtR gene was identified in the place of the cmtI gene of previous annotation. Western blot analysis showed that, in strains F1 and KL47, the todT gene is not expressed during growth on Luria Bertani medium. In minimal basal salt medium, expression of the todT gene is inducible by toluene, but not by biphenyl in strain F1; however, it is constantly expressed in strain KL47, indicating that high levels of expression of the todST genes with one amino acid substitution in TodS might provide strain KL47 with a means of adaptation of the tod catabolic operon to various aromatic hydrocarbons.

• Journal of the Korean Society of Food Science and Nutrition
• /
• v.34 no.8
• /
• pp.1124-1129
• /
• 2005

Functional activities of low molecular weight substances purified from pepsin hydrolysates of four different seaweeds; Costaria costata, Enteromorpha prolifera, Grateloupia filicina and Porphyra tenera, were inves-tigated. Each pepsin hydrolysate of Costaria costata, Enteromorpha prolifera, and Grateloupia filicina resulted in three peptide peaks on Bio-Rad P2 gel chromatography pattern, while that of Porphyra tenera showed 2 peaks. Peak 1 of Porphyra tenera showed the highest antioxidative activity followed by peak 2 of Porphyra tenera and peak 2 of Costaria costata in order Peak 1 of Porphyra tenera showed the highest ACE inhibitory activity followed by peak 3 and peak 2 of Enteromorpha prolifera in order. Peak 1 and peak 2 of Porphyra tenera, and peak 2 of Enteromorpha prolifera showed the highest antityrosinase activity followed by peak 3 of Enteromorpha prolifera. Peak 1 of Enteromorpha prolifera showed the highest antitumor activity followed by peak 2 of Costaria costata, peak 3 of Enteromorpha prolifera, and peak 3 of Grateloupia filicina in order. Porphyra tenera showed the highest functional activities, which is thought to be due to its high protein content. Structure and amino acid sequence of low molecular weight peptide of Porphyra tenera should be analyzed in the further study.

• Journal of Animal Science and Technology
• /
• v.54 no.4
• /
• pp.241-246
• /
• 2012

The goal of this study was to verify the phylogenetic status of the Korean native goats (KNG). We determined the complete sequence of the mitochondrial cytochrome b gene in 48 goats among four populations. We also analyzed genetic variability within goats, and a phylogenetic analysis was performed by comparison with other country's goats. Three nucleotide substitutions were detected, and two of these were missense mutations that occurred due to a substitution of amino acid. Four haplotypes were defined from KNG. Three of these haplotypes were only found in the Chinese goat. However, the other haplotype was KNG-specific. In the phylogenetic analysis, four clades (A~D) were classified among domestic goats, and the KNG was classified into clade 1 that estimated as lineage A based on the D-loop sequence. Each haplotype from the KNG was clustered closely with that of the Chinese goat. The results of haplotype distribution and phylogenetic location suggest that strong gene flow occurred from China to the Korean Peninsula.

• Korean Journal of Microbiology
• /
• v.41 no.4
• /
• pp.255-261
• /
• 2005

A 6.7kb DNA fragment containing the sprT gene encoding Streptomyces griseus trypsin (SGT) was cloned from Streptomyces griseus ATCC 10137, and the complete nucleotide sequence was determined. Nucleotide sequence and deduced amino acid or the EcoRI-HindIII fragment revealed the presence or the six complete ORFs containing the sprT gene and one incomplete ORF, which were named ORF1, SGT, ORF2, ORF3, ORF4, ORF5, and ORF6, respectively. ORF1 has homology with the oxidoreductases from several organisms. ORF2 and ORF3 show similarity with unknown proteins and transcription regulator that belongs to the ArsR family, respectively. ORF4 and ORF5 show homology with the peptidoglycan bound protein with LPXTG motif from Listeria monocytogenes and the membrane protein with transmembrane helix from several organisms, respectively. The last ORF, ORF6, shows homology with the lipoprotein from Streptomyces avermitilis.

• Korean Journal of Microbiology
• /
• v.32 no.2
• /
• pp.102-108
• /
• 1994

Autonomously replicating sequence Binding Factor 1(ABF1) is a DNA-binding protein that specifically recognizes the $RTCRYN_5ACG$ at many sites in the yeast genome including the promoter element, mating-type silencer and ARS. To express the intact full-length ABF1 gene in E. coli, the ABF1 gene has been cloned into pMAL-c2 and His-61, Leu-353 and Leu-360 were substituted with other amino acid. ABF1 fusion proteins of wild type ABF1 and H61A, L353R and L360R nutants were purified by amylose resin affinity chromatography. Fusion protein of MBP and ABF1 was digested by Factor Xa and Characterized by gel retardation assay and complementation test. As aresult, we suggested that other DNA binding motif except atypical inc-finger motif is in the middle region of ABF1.

• The Korean Journal of Mycology
• /
• v.26 no.3 s.86
• /
• pp.354-360
• /
• 1998

We isolated three amplified DNA fragments from P. sajor-caju by Polmerase chain reaction (PCR) using the chithin synthase specific primers. Since the sequence analysis of the these fragments showed significant homology to the other known chitin synthase gene, we regarded these cloned fragments as PsCHS1, PsCHS2, and PsCHS3 according to their size. The PsCHS3, which showed the highest sequence homology (83% identity in amino acid level with ChsI of Rhizopus oligosporus in conserved region), was selected to see expression pattern of the corresponding gene. The result of RT-PCR using internal primer of the PsCHS3 fragment revealed that PsCHS3 gene was only expressed in cap and mycelium but not in stipe. In order to see whether the PsCHS3 gene was to be induced by wounding, the comparison of the mRNA level of this gene between wounded and unwounded mature cap showed at least two times induction of this gene by wounding treatment.