• The Plant Pathology Journal
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• v.24 no.2
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• pp.191-201
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• 2008

Bacillus sp. SB-007 was isolated from pea leaves harvested from the southwestern parts of South Korea through screening on a minimal medium containing 0.2% purified cutin for its ability to induce the cutinase production. However, no cutinase was produced when it was grown in a minimal medium containing 0.2% glucose. A proteomic approach was applied to separate and characterize these differentially secreted proteins. The expression level of 83 extracellular proteins of the cutinase-producing Bacillus sp. strain SB-007 incubated in a cutinase-induced medium increased significantly as compared with that cultured in a non cutinase-induced medium containing glucose. The extracellular proteome of Bacillus sp. SB-007 includes proteins from different functional classes, such as enzymes for the degradation of various macromolecules, proteins involved in energy metabolism, sporulation, transport/binding proteins and lipoproteins, stress inducible proteins, several cellular molecule biosynthetic pathways and catabolism, and some proteins with an as yet unknown function. In addition, the two protein spots showed little similarities with the known lipolytic enzymes in the database. These secreted proteome analysis results are expected to be useful in improving the Bacillus strains for the production of industrial cutinases.

• Journal of Microbiology and Biotechnology
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• v.14 no.6
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• pp.1227-1231
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• 2004

Campylobacter, one of the emerging foodborne pathogens, is highly adaptable to the external environments by changing its morphology. In the present study, a question of whether the whole-cell antibody would still be effective for its detection even though the morphology of C. jejuni was changed was examined. When microaerophilic C. jejuni was exposed to aerobic conditions for 48 h, its morphological change was detected by confocal laser scanning microscope: Its morphology was confirmed as a spiral-bacilli form in microaerobic condition, however, as a coccoid form with a little spiral-bacilli form, when exposed to aerobic conditions. Also, the expressions of the whole-cell proteins of C. jejuni, and the suppression or induction of newly synthesized proteins in both aerobic and microaerobic conditions were analyzed by two dimensional gel electrophoresis. Additionally, immunoblotting assay with the whole cell antibody for the proteins expressed under the two conditions was performed. It was confirmed that the commercial whole-cell antibody of C. jejuni raised in rabbit was reactive. When analyzed with MALDI- TOF MS, the expressed proteins were confirmed as flagellins. Therefore, even though the morphology changed in aerobic condition, these flagellins were expressed and worked as the eitope proteins, thus making it possible to utilize for the development of an immunosensor for real-time detection of any kind of C. jejuni cell.

• Applied Biological Chemistry
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• v.29 no.2
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• pp.175-181
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• 1986

Eightyseven strains of indigenous Rhizobia were isolated from the nodule of soybean cultivar, Danyup, cultivated in four different soils sampled from continuously soybean cultivated and newly reclaimed fields. The strains were grouped into Bradyrhizobium japanicum (slow-grower:55 strains) and Rhizobium fredii (fast-grower: 32 strains). The both groups could be divided into two sub-groups according to the denitrification characteristics, that is, denitrifying fast-grower (F-I), nitrate respiring fast-grower (F-II), denitrifying slow-grower (S-I). and nitrate respiring slow-grower (S-II). Among the 87 isolates, F-I, F-II, S-I and S-II sub-groups were 10, 22, 48 and 7 strains, respectively. The one-and two-dimensional polyacrylamide gel electrophoretic pattern of the four sub-groups were compared and discernible difference was observed between fast and slow-grower, but the difference was not discernible between subgroups within the same growth rate group.

• Journal of Microbiology and Biotechnology
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• v.29 no.11
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• pp.1817-1829
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• 2019

Porcine deltacoronavirus (PDCoV) is an emerging swine enteric coronavirus that causes diarrhea in neonatal piglets. Like other coronaviruses, PDCoV encodes at least three accessory or species-specific proteins; however, the biological roles of these proteins in PDCoV replication remain undetermined. As a first step toward understanding the biology of the PDCoV accessory proteins, we established a stable porcine cell line constitutively expressing the PDCoV NS7 protein in order to investigate the functional characteristics of NS7 for viral replication. Confocal microscopy and subcellular fractionation revealed that the NS7 protein was extensively distributed in the mitochondria. Proteomic analysis was then conducted to assess the expression dynamics of the host proteins in the PDCoV NS7-expressing cells. High-resolution two-dimensional gel electrophoresis initially identified 48 protein spots which were differentially expressed in the presence of NS7. Seven of these spots, including two up-regulated and five down-regulated protein spots, showed statistically significant alterations, and were selected for subsequent protein identification. The affected cellular proteins identified in this study were classified into functional groups involved in various cellular processes such as cytoskeleton networks and cell communication, metabolism, and protein biosynthesis. A substantial down-regulation of α-actinin-4 was confirmed in NS7-expressing and PDCoV-infected cells. These proteomic data will provide insights into the understanding of specific cellular responses to the accessory protein during PDCoV infection.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.265-271
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• 2004

The interaction network of protein -protein plays an important role to understand the various biological functions of cells. Currently, the high -throughput experimental techniques (two -dimensional gel electrophoresis, mass spectroscopy, yeast two -hybrid assay) provide us with the vast amount of data for protein-protein interaction at the proteome scale. In order to recognize the role of each protein in their network, the efficient bioinformatical and computational analysis methods are required. We propose a systematic and mathematical method which can analyze the protein -protein interaction network rigorously and enable us to capture the biological and physical essence of a topological character and stability of protein -protein network, and sensitivity of each protein along the biological pathway of their network. We set up a Laplacian matrix of spectral graph theory based on the protein-protein network of yeast proteome, and perform an eigenvalue analysis and apply a perturbation method on a Laplacian matrix, which result in recognizing the center of protein cluster, the identity of hub proteins around it and their relative sensitivities. Identifying the topology of protein -protein network via a Laplacian matrix, we can recognize the important relation between the biological pathway of yeast proteome and the formalism of master equation. The results of our systematic and mathematical analysis agree well with the experimental findings of yeast proteome. The biological function and meaning of each protein cluster can be explained easily. Our rigorous analysis method is robust for understanding various kinds of networks whether they are biological, social, economical...etc

• Korean Journal of Plant Tissue Culture
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• v.21 no.2
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• pp.123-129
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• 1994

The potency of adventitious root initiation was investigated in relation with germination days and ike end of culture days healed with root induction medium on the initiation of adventitious roots from explants of soybean (Glycine max L.) cotyledon. Also, the changes in the pattern of protein profiles related with adventitious mot initiation have been examined by two-dimensional polyauyl-amide gel elecoophoresis during the germination and the initiation of adventitious roots. The potency of adventitious root initiation from germinated cotyledons was high after 4 days, and adventitious roots were initiated from after 4 days and very high after 6 days healed with mot induction medium There was a reproducible quantitative change in 34 specific protein spots during germination and adventitious root initiation. A necessary basic protein for adventitious root initiation with rotative molecular weight of 27 kD was induced during the germination. And three basic protein groups with relative molecular weight 22 kD, 23 kD and 33 kD, and two acidic protein groups with relative molecular weight 27kD and 29 kD were induced during the initiation of adventitious roots.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.4
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• pp.1667-1674
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• 2012

Objective: To explore the differential protein expression profile in EC304 gastric cancer cells induced by alphastatin. Methods: Cultured EC304 cells in the exponential phase of growth were randomly divided into alphastatin and control groups. Total proteins were extracted and the two dimensional electrophoresis (2-DE) technique was applied to analyze differences in expression with ImageMaster 2D Platinum 5.0 software. Proteins were identified using the MASCOT database and selected differently expressed proteins were characterised by western blotting and immunofluorescence. Results: $1350{\pm}90$ protein spots were detected by the ImageMaster software in the 2-DE gel images from the control and alphastatin groups. The match rate was about 72-80% for the spectrum profiles, with 29 significantly different protein spots being identified, 10 upregulated, 16 downregulated, two new and one lost. The MASCOT search scores were 64-666 and the peptide matching numbers were 3-27 with sequence coverage of 8-62%. Twenty-three proteins were checked by mass spectrometry, including decrease in Nm23 and profilin-2 isoform b associated with the regulation of actin multimerisation induced by extracellular signals. Conclusion: The proteome in EC304 cells is dramatically altered by alphastatin, which appears to play an important role in modulating cellular activity and anti-angiogenesis by regulating protein expression and signal transduction pathways through Nm23 and profilin-2 isoform b, providing new research directions for anti-angiogenic therapy of gastric cancer.

• Journal of Microbiology and Biotechnology
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• v.20 no.3
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• pp.532-541
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• 2010

Peroxidase-like activity of Vitreoscilla hemoglobin (VHb) has been recently disclosed. To maximize such activity, two catalytically conserved residues (histidine and arginine) found in the distal pocket of peroxidases have successfully been introduced into that of the VHb. A 15-fold increase in catalytic constant ($k_{cat}$) was obtained in P54R variant,which was presumably attributable to the lower rigidity and higher hydrophilicity of the distal cavity arising from substitution of proline to arginine. None of the modifications altered the affinity towards either $H_2O_2$ or ABTS substrate. Spectroscopic studies revealed that VHb variants harboring the T29H mutation apparently demonstrated a spectral shift in both ferric and ferrous forms (406-408 to 411 nm, and 432 to 424-425 nm, respectively). All VHb proteins in the ferrous state had a $\lambda_{soret}$ peak at ~419 nm following the carbon monoxide (CO) binding. Expression of the P54R mutant mediated the downregulation of iron superoxide dismutase (FeSOD) as identified by two-dimensional gel electrophoresis (2-DE) and peptide mass fingerprinting (PMF). According to the high peroxidase activity of P54R, it could effectively eliminate autoxidation-derived $H_2O_2$, which is a cause of heme degradation and iron release. This decreased the iron availability and consequently reduced the formation of the $Fe^{2+}$-ferric uptake regulator protein ($Fe^{2+}$-Fur), an inducer of FeSOD expression.

• Journal of Crop Science and Biotechnology
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• v.10 no.2
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• pp.112-116
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• 2007

Kinetin(KN) is an inducer of rice(Oryza sativa L.) defense/stress responses, as evidenced by the induction of inducible secondary metabolite and defense/stress protein markers in leaf. We show a novel light-dependent effect of KN-triggered defense stress responses in rice leaf. Leaf segments treated with KN(100 ${\mu}M$) show hypersensitive-like necrotic lesion formation only under continuous light illumination. Potent accumulation of two phytoalexins, sakuranetin and momilactone A(MoA) by KN that peaks at 48 h after treatment under continuous light is completely suppressed by incubation under continuous dark. Using two-dimensional gel electrophoresis we identified KN-induced changes in ribulose-1, 5-bisphosphate carboxylase/oxygenase, energy- and pathogenesis-related proteins(OsPR class 5 and 10 members) by N-terminal amino acid sequencing and mass spectrometry. These changes were light-inducible and could not be observed in the dark(and control). Present results provide a new dimension(light modulation/regulation) to our finding that KN has a potential role in the rice plant self-defense mechanism.

• The Plant Pathology Journal
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• v.35 no.4
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• pp.313-320
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• 2019

Rye was used here to dissect molecular mechanisms of resistance to Fusarium head blight (FHB) and to go deeper with our understanding of that process in cereals. F. culmorum-damaged kernels of two lines different in their potential of resistance to FHB were analyzed using two-dimensional gel electrophoresis and mass spectrometry to identify resistance markers. The proteome profiling was accompanied by measurements of ${\alpha}-$ and ${\beta}-amylase$ activities and mycotoxin content. The proteomic studies indicated a total of 18 spots with clear differences in protein abundance between the more resistant and more susceptible rye lines after infection. Eight proteins were involved in carbohydrate metabolism of which six proteins showed a significantly higher abundance in the resistant line. The other proteins recognized here were involved in stress response and redox homeostasis. Three remaining proteins were associated with protease inhibition/resistance and lignin biosynthesis, revealing higher accumulation levels in the susceptible rye line. After inoculation, the activities of ${\alpha}-$ and ${\beta}-amylases$, higher in the susceptible line, were probably responsible for a higher level of starch decomposition after infection and a higher susceptibility to FHB. The presented results could be a good reference for further research to improve crop resistance to FHB.