• BMB Reports
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• 제38권5호
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• pp.571-576
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• 2005

Cytokines are proteins produced by many different cells of the immune system and play a significant role in initiating and regulating the inflammatory process. In this research, an important cytokine, interleukin-10 (IL-10) gene, has been identified and characterized from zebrafish (Danio rerio) genome database. Zebrafish IL-10 is located within a 2690 bp fragment and contains five exons and four introns, sharing the same organization with mammalian IL-10 genes. An open reading frame of 543 bp was found to encode a putative 180 amino acid protein with a signal peptide of 22 amino acids, which shares 29.7-80.9% homology with amino acid sequences of other known IL-10. The signature motif of IL-10 is also conserved in zebrafish IL-10. The predicted transcript was finally confirmed by sequencing of cDNA clones. Multi-tissue reverse transcriptase PCR (RT-PCR) was performed to examine the tissue distribution and expression regulation of this gene in seven organs of normal and lipopolysaccharide (LPS) stimulation zebrafish. The results demonstrated that this gene was expressed slightly in normal kidney, gill and gut, no expression was detected in other four tissues. The expression was clearly upregulated after LPS stimulation. Using the ideal zebrafish model, further study of IL-10 characterization and function may provide insight on the understanding of the innate immune system.

• Journal of Microbiology and Biotechnology
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• 제20권12호
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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.

• 한국축산식품학회지
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• 제36권2호
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• pp.254-261
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• 2016

The purpose of this study was to analyze oxidized methionines in the myosin isoforms of porcine longissimus thoracis, psoas major, and semimembranosus muscles by liquid chromatography (LC) and mass spectrometry (MS). A total of 836 queries matched to four myosin isoforms (myosin-1, -2, -4, and -7) were analyzed and each myosin isoform was identified by its unique peptides (7.3-13.3). Forty-four peptides were observed from all three muscles. Seventeen peptides were unique to the myosin isoform and the others were common peptides expressed in two or more myosin isoforms. Five were identified as oxidized peptides with one or two methionine sulfoxides with 16 amu of mass modification. Methionines on residues 215 (215), 438 (438), 853 (851), 856 (854), 1071 (1069), and 1106 (1104) of myosin-1 (myosin-4) were oxidized by the addition of oxygen. Myosin-2 had two oxidized methionines on residues 215 and 438. No queries matched to myosin-7 were observed as oxidized peptides. LC-MS/MS allows analysis of the oxidation of specific amino acids on specific residue sites, as well as in specific proteins in the food system.

• 원예과학기술지
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• 제34권1호
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• pp.46-54
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• 2016

2-Oxoglutarate (2OG) acts as a signaling molecule and plays a critical role in secondary metabolism in a variety of organisms, including plants. Six 2-oxoglutarate (2OG) and Fe(II) oxygenase (2OGO) genes, VlCE2OGO1 [Vitis labruscana 2-oxoglutarate (2OG) and Fe(II) oxygenase 1], VlCE2OGO2, VlCE2OGO3, VlCE2OGO4, VlCE2OGO5, and VlCE2OGO6, which show different expression patterns upon transcriptome analysis of 'Campbell Early' grapevine exposed to low temperature for 4 weeks, were analyzed for their structure and expression. Comparison of the deduced amino acid sequences of the 2OGO genes from the V. labruscana transcripts revealed sequence similarities of 38.6% (VlCE2OGO1 and VlCE2OGO2) to 19.2% (VlCE2OGO2 and VlCE2OGO3). The lengths of these genes ranged from 1053 to 2298 bp, and they encoded 316 to 380 amino acids. The prediction of the secondary structure of the encoded proteins by Self-Optimized Prediction Method with Alignment (SOPMA) indicated that all the genes contained alpha helix (23.95 to 41.71%), extended strand (16 to 22.34%), beta turn (6.65 to 9.22%), and random coil (32.97 to 51.58%) in the analysis. Specific primers from unique regions in each gene obtained by alignment of nucleotide sequences were used in real time PCR for analysis of gene expression. All tested genes showed differential expression in grapevines exposed to low temperature. Of the six transcripts, VlCE2OGO1, VlCE2OGO2, and VlCE2OGO3 were up-regulated and VlCE2OGO4, VlCE2OGO5, and VlCE2OGO6 were down-regulated in response to cold treatments at all tested time points. The 2OG genes can be used for elucidation of mechanisms of tolerance to cold and as valuable molecular genetic resources for selection in breeding programs for cold-hardy grapevines.

• Mass Spectrometry Letters
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• 제14권4호
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• pp.147-152
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• 2023

The increasing demand for two-dimensional imaging analysis using optical or electronic microscopic techniques has led to an increase in the use of simple one-dimensional and two-dimensional mass spectrometry imaging. Among these imaging methods, secondary-ion mass spectrometry (SIMS) has the best spatial resolution using a primary ion beam with a relatively insignificant beam diameter. Until recently, SIMS, which uses high-energy primary ion beams, has not been used to analyze molecules. However, owing to the development of cluster ion beams, it has been actively used to analyze various organic molecules from the surface. Researchers and commercial SIMS companies are developing cluster ion beams to analyze biological samples, including amino acids, peptides, and proteins. In this study, a water droplet ion beam for surface analysis was realized. Water droplets ions were generated via electrospraying in a vacuum without desolvation. The generated ions were accelerated at an energy of 10 keV and collided with the target sample, and secondary ion mass spectra were obtained for the generated ions using ToF-SIMS. Thus, the proposed water droplet ion-beam device showed potential applicability as a primary ion beam in SIMS.

• The Plant Pathology Journal
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• 제32권4호
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• pp.347-356
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• 2016

Plants protect themselves from pathogen attacks via several mechanisms, including hypersensitive cell death. Recognition of pathogen attack by the plant resistance gene triggers expression of carboxylesterase genes associated with hypersensitive response. We identified six transcripts of carboxylesterase genes, Vitis flexuosa carboxylesterase 5585 (VfCXE5585), Vf-CXE12827, VfCXE13132, VfCXE17159, VfCXE18231, and VfCXE47674, which showed different expression patterns upon transcriptome analysis of V. flexuosa inoculated with Elsinoe ampelina. The lengths of genes ranged from 1,098 to 1,629 bp, and their encoded proteins consisted of 309 to 335 amino acids. The predicted amino acid sequences showed hydrolase like domains in all six transcripts and contained two conserved motifs, GXSXG of serine hydrolase characteristics and HGGGF related to the carboxylesterase family. The deduced amino acid sequence also contained a potential catalytic triad consisted of serine, aspartic acid and histidine. Of the six transcripts, Vf-CXE12827 showed upregulated expression against E. ampelina at all time points. Three genes (VfCXE5585, VfCXE12827, and VfCXE13132) showed upregulation, while others (VfCXE17159, VfCXE18231, and VfCXE47674) were down regulated in grapevines infected with Botrytis cinerea. All transcripts showed upregulated expression against Rhizobium vitis at early and later time points except VfCXE12827, and were downregulated for up to 48 hours post inoculation (hpi) after upregulation at 1 hpi in response to R. vitis infection. All tested genes showed high and differential expression in response to pathogens, indicating that they all may play a role in defense pathways during pathogen infection in grapevines.

• BMB Reports
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• 제41권4호
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• pp.338-343
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• 2008

Dehydrins (DHNs) compose a family of intrinsically unstructured proteins that have high water solubility and accumulate during late seed development at low temperature or in water-deficit conditions. They are believed to play a protective role in freezing and drought-tolerance in plants. A full-length cDNA encoding DHN (designated as ClDhn) was isolated from an oriental medicinal plant Codonopsis lanceolata, which has been used widely in Asia for its anticancer and anti-inflammatory properties. The full-length cDNA of ClDhn was 813 bp and contained a 477 bp open reading frame (ORF) encoding a polypeptide of 159 amino acids. Deduced ClDhn protein had high similarities with other plant DHNs. RT-PCR analysis showed that different abiotic stresses such as salt, wounding, chilling and light, triggered a significant induction of ClDhn at different time points within 4-48 hrs post-treatment. This study revealed that ClDhn assisted C. lanceolata in becoming resistant to dehydration.

• Journal of Plant Biotechnology
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• 제47권4호
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• pp.316-323
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• 2020

본 연구는 제초제저항성 GM 들잔디에서 발현된 PAT 단백질의 잠재적인 알레르기성 및 독성을 평가하기 위해 수행되었다. PAT 단백질의 in silico 분석에서 PAT 단백질은 알려진 알레르겐 또는 독성 단백질과 유사성을 보이지 않았다. PAT 단백질은 80개의 아미노산으로 이루어진 절편에 걸쳐 기지의 알레르겐과 35% 미만의 아미노산 서열 상동성을 보였고, 기지의 알레르겐과 연속한 8개의 아미노산에서 일치하는 서열도 확인되지 않았다. 또한 제초제저항성 GM 들잔디에서 발현된 PAT 단백질은 펩신 존재 하의 인공위액에서 매우 빠르게 분해되었고, GM 들잔디에서 발현된 PAT 단백질은 번역 후 수식(glycosylation)도 일어나지 않았음이 확인되었다. 경구투여 독성 시험에서는 체중 1 kg 당 4,000 mg 을 투여한 실험구에서도 PAT 단백질 투여 후 마우스에서 사망이나 독성 영향은 관찰되지 않았다. 이들 결과는 제초제저항성 GM 들잔디에서 발현된 PAT 단백질이 잠재적 알레르겐이나 독소로 작용할 가능성이 없음을 시사한다.

• BMB Reports
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• 제37권2호
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• pp.159-166
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• 2004

Angiostatin is a potent anti-angiogenic protein. To examine the angiostatin-interacting proteins, we used the display-cloning method with a T7 phage library presenting human cDNAs. The specific T7 phage clone that bound to the immobilized angiostatin was isolated, and a novel gene encoding the displayed polypeptide on the isolated T7 phage was identified. The displayed angiostatin-binding sequence was expressed in E. coli as a soluble protein and purified to homogeneity. This novel angiostatin-binding region interacted specifically to angiostatin with a dissociation constant of $3.4{\times}10^{-7}\;M$. A sequence analysis showed that the identified sequence was a part of the large ORF of 1,998 amino acids, whose function has not yet been characterized. A Northern analysis indicated that the gene containing the angiostatin-binding sequence was expressed differentially in the developmental stages or cell types.

• Journal of Applied Biological Chemistry
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• 제44권1호
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• pp.6-11
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• 2001

An ${\omega}-3$ fatty acid desaturase gene which is involved in de novo synthesis of -Iinolenate was isolated from cDNA library of Perilla frutescens. A cDNA library was constructed with mRNA extracted from perilla seeds of 12 DAF. The cDNA clone consisting of 1317-bp open reading frame encoding 438 amino acids with a relative MW of 50kDa, was isolated and showed 65-83% similarities to other known genes. This cDNA is deduced to encode a plastidal ${\omega}-3$ fatty acid desaturase based on the fact that it has higher homology to plastidal ones than to microsomal ones and its N-terminal sequence shares several characteristics of transit peptides of chloroplast proteins. Southern blot analysis of genomic DNA indicated that more than one gene or alleles for ${\omega}-3$ fatty acid desaturase are present in the genome of perilla. Northern blot analysis showed that the ${\omega}-3$ fatty acid desaturase gene is mainly revealed in early developing seeds and has different expression patterns depending on tissue types compared to the microsomal ones.