• Bulletin of the Korean Chemical Society
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• 제29권1호
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• pp.173-176
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• 2008

MJ0684 from Methanococcus jannaschii is a hypothetical protein belonging to the subfamily Ig of amino acid aminotransferases. In the present study, the crystal structure of MJ0684 has been determined at 2.2 resolution. It reveals that MJ0684 has an overall structure similar to subfamily Ig aminotransferases and its active site architecture is most similar to that of kynurenine aminotransferases among several kinds of aminotransferases in the subfamily Ig?. It has two hydrophobic active site residues conserved in the kynurenine aminotransferases for recognizing hydrophobic substrates. In addition, the absence of any basic residue for recognizing the side chain carboxylic group of the aspartate in the active site rules out the possibility that MJ0684 would act as an aspartate aminotransferase. These structural observations collectively imply that MJ0684 is a novel archaeal homolog of the subfamily Ig kynurenine aminotransferase.

• Parasites, Hosts and Diseases
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• 제45권4호
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• pp.283-285
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• 2007

To examine the expressed gene profile during encystation of Acanthamoeba castellanii Castellani, we used differentially expressed gene (DGE) screening by RT-PCR with 20 sets of random primers. From this analysis, we found that approximately 16 genes showed up regulation during encystation. We chose 6 genes, which had relatively higher expression levels, for further investigation. Based on homology search in database, DEG2 showed 55% of similarity with xylose isomerase, DEG9 showed 37% of similarity with Na P-type ATPase, and DEG14 showed 77% of similarity with subtilisin-like serine proteinase. DEG3 and DEG26 were identified as hypothetical proteins and DEG25 exhibited no significant similarity to any known protein. Encystation of Acanthamoeba has been suggested to be a process to resist adverse environmental or nutritional conditions. Further characterization studies of these genes may provide us with more information on the encystation mechanism of Acanthamoeba.

• Journal of Microbiology and Biotechnology
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• 제16권6호
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• pp.946-951
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• 2006

To study the effect of iron on Saccharomyces cerevisiae, whole-cell proteins of Saccharomyces cerevisiae were extracted and subjected to two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and differentially expressed proteins were identified. The proteins separated were further identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and were compared with a protein database. Of more than 300 spots separated by molecular weight and isoelectric points, 27 differentially expressed spots were identified. Ten proteins were found to be differentially expressed at high iron concentration. Triosephosphate isomerase (TPI), YDR533C hypothetical protein, superoxide dismutase (SOD), 60 kDa heat-shock protein (HSP60), pyruvate dehydrogenase beta subunit 1 (PDB1), and old yellow enzyme 2 (OYE2) were upregulated, whereas thiol-specific antioxidant (TSA), regulatory particle non-ATPase subunit 8 (RPN8), thiol-specific peroxiredoxin 1 (AHP1), and fructose-1, 6-bisphosphate adolase (FBA) were downregulated by iron. Based on the result, we propose that SOD upregulated by iron would protect the yeast from oxidative stress by iron, and that TSA downregulated by iron would render cells hypersensitive to oxidative stress.

• Journal of Microbiology and Biotechnology
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• 제29권3호
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• pp.500-505
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• 2019

Staphylococcus aureus is a round-shaped, gram-positive bacterium that can cause numerous infectious diseases ranging from mild infections such as skin infections and food poisoning to life-threatening infections such as sepsis, endocarditis and toxic shock syndrome. Various antibiotic-resistant strains of S. aureus have frequently emerged, threatening human lives significantly. Despite much research on the genetics of S. aureus, many of its genes remain unknown functionally and structurally. To counteract its toxins and to prevent the antibiotic resistance of S. aureus, our understanding of S. aureus should be increased at the proteomic scale. SAV0927 was first sequenced in an antibiotic resistant S. aureus strain. The gene is a conserved hypothetical protein, and its homologues appear to be restricted to Firmicutes. In this study, we determined the crystal structure of SAV0927 at $2.5{\AA}$ resolution. The protein was primarily dimeric both in solution and in the crystals. The asymmetric unit contained five dimers that are stacked linearly with ${\sim}80^{\circ}$ rotation by each dimer, and these interactions further continued in the crystal packing, resulting in a long linear polymer. The crystal structures, together with the network analysis, provide functional implications for the SAV0927-mediated protein network.

• 미생물학회지
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• 제52권1호
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• pp.110-115
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• 2016

남극 해양세균 Pseudoalteromonas sp. PAMC 21150에서 분리한 소형 플라스미드(small plasmid, pDK4)의 크기는 3,480bp이고 G+C 함량은 41.64%이며, 3개의 open reading frames(ORFs)을 포함하고 있다. 3개의 ORF는 replication initiation protein (RepA), conjugative mobilization protein (Mob), 그리고 기능이 밝혀지지 않은 단백질을 코팅하고 있다. PCR 반응으로 증폭한 pDK4를 Escherichia coli high-copy pUC19 클로닝 벡터에 삽입하여 fusion vector (pDOC153)를 제작하였고, pDOC 153에 chloramphenicol 저항성 유전자를 삽입하여 ampicillin/chloramphenicol 저항성 Pseudoalteromonas - Escherichia coli 셔틀 벡터(shuttle vector; 7,216 bp 크기; pDOC155)를 제작하였다. 북극 해양세균 P. issachenkonii PAMC 22718이 보유한 2개의 유전자(TonB-dependent receptor gene, chi22718_IV, and exochitinase gene, chi22718_III)를 pDOC155에 삽입하여 두 개의 pDOC155 변형체(pDOC158, pDOC165)를 제작하였다. pDOC158 혹은 pDOC165을 이용하여 triparental mating 방법에 의해 플리스미드 미보유 해양세균인 Pseudoalteromonas sp. PAMC 22137를 형질전환하였다. PCR을 이용한 유전자 증폭실험을 통해서, pDOC158와 pDOC165에 삽입된 유전자들은 Pseudoalteromonas sp. PAMC 22137와 E. coli $DH5{\alpha}$ 내에서 안정적으로 유지되는 것을 확인하였다. 위의 결과는 셔틀 벡터 pDOC155는 Pseudoalteromonas spp. 유래 유전자들을 다른 Pseudoalteromonas spp. 세포 안으로 전달할 수 있는 새로운 유전자 전달시스템으로 이용될 수 있음을 보여주었다.

• ALGAE
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• 제26권1호
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• pp.87-96
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• 2011

Protein profiles of a common mixotrophic dinoflagellate, Prorocentrum micans, growing autotrophically and mixotrophically (fed on the cryptophyte Rhodomonas salina) were compared using two-dimensional gel electrophoresis (2-DE) to determine if they vary in different trophic modes. Approximately 2.3% of the detected proteins were differentially expressed in the different trophic modes. Twelve proteins observed only in the mixotrophic condition had lower pI value (<5) than the fifteen proteins observed only in the autotrophic condition (>5). When the internal amino acid sequences of five selected proteins differentially expressed between autotrophic and mixotrophic conditions were analyzed using matrix-assisted laser desorption time-of-flight (MALDI-TOF) mass spectrometry, two proteins that were specifically expressed in the autotrophic condition showed homology to glyceraldehyde-3-phosphatase dehydrogenase (GAPDH) and a bacterial catalase. Three mixotrophy-specific proteins showed homology to certain hypothetical proteins from an insect and bacteria. These results suggested the presence of certain gene groups that are switched on and off according to the trophic mode of P. micans.

• 한국자기공명학회논문지
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• 제19권1호
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• pp.49-53
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• 2015

MRA1997 is a 76-residue conserved hypothetical protein of Mycobacterium tuberculosis H37Ra, one of the most pathogenic bacterial species and the causative agent of tuberculosis. In this study, the sequence-specific backbone resonance assignment of MRA1997 was performed using NMR spectroscopy. Approximately 88.3% of the total resonances could be unambiguously assigned. By analyzing deviations of the $C{\alpha}$ and $C{\beta}$ chemical shift values, the secondary structure of MRA1997 was calculated. The result revealed that secondary structure of MRA 1997 consists of one ${\alpha}$-helix and five ${\beta}$-sheets. Our structural study will be a footstone towards the characterization of the three-dimensional structure of MRA1997.

• Journal of Microbiology and Biotechnology
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• 제20권4호
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• pp.789-797
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• 2010

The limited information on differential gene expression in the different serotypes of Actinobacillus pleuropneumoniae has significantly hampered the research on the pathogenic mechanisms of this organism and the development of multivalent vaccines against A. pleuropneumoniae infection. To compare the gene expressions in the A. pleuropneumoniae strains CVCC259 (serotype 1) and CVCC261 (serotype 3), we screened the differentially expressed genes in the two strains by performing representational difference analysis (RDA). Northern blot analyses were used to confirm the results of RDA. We identified 22 differentially expressed genes in the CVCC259 strain and 20 differentially expressed genes in the CVCC261 strain, and these genes were classified into 11 groups: (1) genes encoding APX toxins; (2) genes encoding transferrin-binding protein; (3) genes involved in lipopolysaccharide (LPS) biosynthesis; (4) genes encoding autotransporter adhesin; (5) genes involved in metabolism; (6) genes involved in the ATP-binding cassette (ABC) transporter system; (7) genes encoding molecular chaperones; (8) genes involved in bacterial transcription and nucleic acid metabolism; (9) a gene encoding protease; (10) genes encoding lipoprotein/membrane protein; and (11) genes encoding various hypothetical proteins. This is the first report on the systematic application of RDA for the analysis of differential gene expression in A. pleuropneumoniae serotypes 1 and 3. The determination of these differentially expressed genes will serve as an indicator for future research on the pathogenic mechanisms of A. pleuropneumoniae and the development of a multivalent vaccine against A. pleuropneumoniae infection.

• Journal of Microbiology and Biotechnology
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• 제22권8호
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• pp.1044-1053
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• 2012

The gene encoding an esterase enzyme was cloned from a metagenomic library of cow rumen bacteria. The esterase gene (est5S) was 1,026 bp in length, encoding a protein of 366 amino acid residues with a calculated molecular mass of 40,168 Da. The molecular mass of the enzyme was estimated to be 40,000 Da. The Est5S protein contains the Gly-X-Ser-X-Gly motif found in most bacterial and eukaryotic serine hydrolases. However, the Asp or Glu necessary for the catalytic triad [Ser-Asp-(Glu)-His] was not present, indicating Est5S represents a novel member of the GHSQG family of esterolytic enzymes. BlastP in the NCBI database analysis of Est5S revealed homology to hypothetical proteins and it had no homology to previous known lipases and esterases. Est5S was optimally active at pH 7.0 and $40^{\circ}C$. Among the p-nitrophenyl acylesters tested, high enzymatic activities were observed on the short-chain p-nitrophenyl acylesters, such as p-nitrophenyl acetate, etc. The conserved serine residue ($Ser_{190}$) was shown to be important for Est5S activity. The primers that amplified the est5S gene did not show any relative band with 49 species of culturable rumen bacteria. This implies that a new group esterase gene, est5S, may have come from a noncultured cow rumen bacterium.

• 대한한방내과학회지
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• 제28권1호
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• pp.133-148
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• 2007

Objectives : The purpose of our study was to investigate the effects of Injinchunggan-tang (Yinchenchinggan-tang) on DMN liver damage caused by applying proteomics. Materials and Methods: Sprague-Dawley rats were used in this experiment; the rats were divided into the normal group (normal saline), the control group (DMN) and the samplegroup (DMN+IJCGT). The DMN was induced 3 days a week for 3 weeks in the control group. The normal saline without DMN was induced by the same method in the normal group. Injinchunggan-tang extract was orally administered twice a day for 3 weeks after DMN was induced in the sample group. The livers of each group were processed and we investigated histology, OxyBlot, 2-dimensional electrophoresis, and western blot of liver of each group. Results : In the histological findings of the liver, the control group showed portal fibrosis with a few septa or without septa. The sample group showed no fibrosis or portal fibrosis without septa. In the OxyBlot finding, Injinchunggan-tang prevented liver damage by oxidation. In the 2-dimensional electrophoresis finding, formiminotransferase cyclodeaminase (FTCD), FYVE-finger containing protein, aldehyde dehydrogenase (ALDH), and ratio of predicted : hypothetical protein LOC68668 isoform 1 were changed. Conclusions : Injinchunggan-tang exerts an inhibitory effect against the fibrosis and oxidation induced by the DMN in the rat liver cell, and some proteins induced by the DMN were changed by Injinchunggan-tang.