• Journal of Microbiology and Biotechnology
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• v.11 no.6
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• pp.1111-1114
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• 2001

An extracellular fibrinolytic-enzyme-producing bacterium was isolated from Doen-Jang, a Korean traditional fermented flood, and identified as Bacillus sp. DJ based on its morphology and cellular fatty acid composition. The total extracellular fibrinase (EF) from Bacillus sp. DJ was analyzed using three fibrin zymographic techniques, SDS-fibrin zymography (SDS-FZ), isoelectrofocucing-fibrin zymographs(IEF-FZ), and a two-dimensional SDS-fibrin zymographic analysis (2D SDS-FZ). As a result, the EP map of Bacillus sp. DJ was established. The results suggest that the 2D SDS-FZ method will be a useful tool for the proteomic approach for many other bacterial pretenses.

• Journal of Microbiology and Biotechnology
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• v.17 no.2
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• pp.359-363
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• 2007

Because of the importance of the type III protein-secretion system in bacteria-plant interaction, its function in bacterial pathogenesis of plants has been intensively studied. To identity bacterial proteins interacting with Xanthomonas hrp gene products that are involved in pathogenicity, we performed the glutathione-bead binding analysis of Xanthomonas lysates containing GST-tagged Hrp proteins. Analysis of glutathione-bead bound proteins by 1-DE and MALDI-TOF has demonstrated that Avr proteins, RecA, and several components of the type III secretion system interact with HrpB protein. This proteomic approach could provide a powerful tool in finding interaction partners of Hrp proteins whose roles in host-pathogen interaction need further studies.

• BMB Reports
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• v.37 no.1
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• pp.45-52
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• 2004

The goal of interaction proteomics that studies the protein-protein interactions of all expressed proteins is to understand biological processes that are strictly regulated by these interactions. The availability of entire genome sequences of many organisms and high-throughput analysis tools has led scientists to study the entire proteome (Pandey and Mann, 2000). There are various high-throughput methods for detecting protein interactions such as yeast two-hybrid approach and mass spectrometry to produce vast amounts of data that can be utilized to decipher protein functions in complicated biological networks. In this review, we discuss recent developments in analytical methods for large-scale protein interactions and the future direction of interaction proteomics.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.60 no.1
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• pp.29-32
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• 2015

Two-dimensional electrophoresis (2-DE) was executed to separate the seed storage proteins from the buckwheat. The proteins extracted from the whole seed proteins were better separated and observed in the use of lysis buffer. Using this method, the highly reproducible isoelectric focusing (IEF) can be obtained from polyacrylamide gels, and IEF from the polyacrylamide gel at all the possible pH range (5.0-8.0) was more easily separated than IPG (immobilized pH gradient) gels. The polyacrylamide gels in the first dimension in 2-DE was used to separate and identify a number of whole seed proteins in the proteome analysis. In this new apparatus using 2-DE, 27cm in length of plate coated with polyacrylamide gel was used and the experiment was further investigated under the various conditions.

• Reproductive and Developmental Biology
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• v.37 no.4
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• pp.247-253
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• 2013

Here, we present an approach of blood plasma proteome profiling and their comparisons between the young and the adult pigs as prerequisite for the identification of bio-markers related to the health conditions, growth performance and meat quality. To profile the proteome in porcine plasma, blood samples were collected from 19 young piglets and 20 adult male barrows and the plasma was retrieved. Then, protein profiling was initiated using one and two-dimensional electrophoresis. Proteins were spotted and then identified by MALDI-TOF-TOF and LC-MS-MS. In the results, more than thirty-six and twenty eight protein spots were selected in young piglets and adult pigs, respectively and twenty three proteins were identified. The proteome profile images were compared between those ones using Image Master Version 7.0. The image of expressed proteome showed that most of proteins from plasma of young piglet separated clearly and concentrated in 2DE display compared to ones from adult. Image analysis in detail was carried out to look for the specific proteins related to age progression. It demonstrated that the characteristics of proteome expression could be distinct to their age stages. Further investigations needed to proceed to understand the age dependent change of protein conformation and biological meaning of those differences in proteome expression between young and mature adult pigs.

• Genomics & Informatics
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• v.21 no.1
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• pp.5.1-5.13
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• 2023

Neisseria gonorrhoeae is a Gram-negative aerobic diplococcus bacterium that primarily causes sexually transmitted infections through direct human sexual contact. It is a major public health threat due to its impact on reproductive health, the widespread presence of antimicrobial resistance, and the lack of a vaccine. In this study, we used a bioinformatics approach and performed subtractive genomic methods to identify potential drug targets against the core proteome of N. gonorrhoeae (12 strains). In total, 12,300 protein sequences were retrieved, and paralogous proteins were removed using CD-HIT. The remaining sequences were analyzed for non-homology against the human proteome and gut microbiota, and screened for broad-spectrum analysis, druggability, and anti-target analysis. The proteins were also characterized for unique interactions between the host and pathogen through metabolic pathway analysis. Based on the subtractive genomic approach and subcellular localization, we identified one cytoplasmic protein, 2Fe-2S iron-sulfur cluster binding domain-containing protein (NGFG RS03485), as a potential drug target. This protein could be further exploited for drug development to create new medications and therapeutic agents for the treatment of N. gonorrhoeae infections.

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.323.1-323.1
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• 2002

Apicidin ［cyclo(N-O-methyl-l -tryptophanyl-L -isoleucinyl-D-pipecolinyl-L-2-amino-8-oxodecano y)］. a histone deacetylase inhibitor. has been shown to cause growth arrest and morphological change of cancer cells. resulting from the alternation of protein expression. such as p21WAF1/Cip1 and gelsolin. However. proteome of altered by apicidin are poorly studied. In this study. we used a functional proteornics approach to identify the proteome altered by apicidin in Hela cells at 24hr post-treatment. (omitted)

• BMB Reports
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• v.37 no.3
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• pp.298-303
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• 2004

In general, a SYPRO Ruby dye is well known as a sensitive fluorescence-based method for detecting proteins by one-or two-dimensional SDS-PAGE (1-DE or 2-DE). Based on the SYPRO Ruby dye system, the combined two-dimensional fibrin zymography (2-D FZ) with SYPRO Ruby staining was newly developed to identify the Bacillus sp. proteases. Namely, complex protein mixtures from Bacillus sp. DJ-4, which were screened from Doen-Jang (Korean traditional fermented food), showed activity on the zymogram gel. The gel spots on the SYPRO Ruby gel, which corresponded to the active spots showing on the 2-D FZ gel, were analyzed by a matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometric analysis. Five intracellular fibrinolytic enzymes of Bacillus sp. DJ-4 were detected through 2-D FZ. The gel spots on the SYPRO Ruby dye stained 2-D gel corresponding to 2-D FZ were then analyzed by MALID TOF MS. Three of the five gel spots proved to be quite similar to the ATP-dependent protease, extracellular neutral metalloprotease, and protease of Bacillus subtilis. Also, the extracellular proteases of Bacillus sp. DJ-4 employing this combined system were identified on three gels (e.g., casein, fibrin, and gelatin) and the proteolytic maps were established. This combined system of 2-D zymography and SYPRO Ruby dye should be useful for searching the specific protease from complex protein mixtures of many other sources (e.g., yeast and cancer cell lines).

• 한국생물공학회:학술대회논문집
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• 2001.11a
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• pp.750-753
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• 2001

Proteomics is a formalized approach for obtaining a rapid snap-shot of the protein complement of a tissue, cell or cell component. Such an approach is powerful in that it allows a parallel assessment of temporal protein fluxes. This is an important concept in view of the dynamic nature of protein expression. Undoubtedly, changes in protein expression are essential in any study aimed at investigating cellular networks. In this study, we analyzed and compared the proteomes of recombinant E. coli strain before and after induction. Proteome expression patterns of recombinant E. coli were resolved on 2D-gels, and the variations in the relative expression level of particular proteins were examined using software-aided protein quantification tool. We observed above 800 spots on a 2D-gel using Melanie II software. Many proteins which involved in chaperones were significantly up-regulated in recombinant E. coli. Therefore, it could be concluded that the expression of recombinant protein in E. coli acted as a stress to the cells, which change cells ability to synthesize proteins and induced the expression of various protective proteins.

• Proceedings of the Korean Society of Crop Science Conference
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• 2004.04a
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• pp.12-27
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• 2004

Thanks to spectacular advances in the techniques for identifying proteins separated by two-dimensional electrophoresis and in methods for large-scale analysis of proteome variations, proteomics is becoming an essential methodology in various fields of plant sciences. Plant proteomics would be most useful when combined with other functional genomics tools and approaches. A combination of microarray and proteomics analysis will indicate whether gene regulation is controlled at the level of transcription or translation and protein accumulation. In this review, we described the catalogues of the rice proteome which were constructed in our program, and functional characterization of some of these proteins was discussed. Mass-spectrometry is a most prevalent technique to identify rapidly a large of proteins in proteome analysis. However, the conventional Western blotting/sequencing technique us still used in many laboratories. As a first step to efficiently construct protein data-file in proteome analysis of major cereals, we have analyzed the N-terminal sequences of 100 rice embryo proteins and 70 wheat spike proteins separated by two-dimensional electrophoresis. Edman degradation revealed the N-terminal peptide sequences of only 31 rice proteins and 47 wheat proteins, suggesting that the rest of separated protein spots are N-terminally blocked. To efficiently determine the internal sequence of blocked proteins, we have developed a modified Cleveland peptide mapping method. Using this above method, the internal sequences of all blocked rice proteins (i. e., 69 proteins) were determined. Among these 100 rice proteins, thirty were proteins for which homologous sequence in the rice genome database could be identified. However, the rest of the proteins lacked homologous proteins. This appears to be consistent with the fact that about 30% of total rice cDNA have been deposited in the database. Also, the major proteins involved in the growth and development of rice can be identified using the proteome approach. Some of these proteins, including a calcium-binding protein that fumed out to be calreticulin, gibberellin-binding protein, which is ribulose-1,5-bisphosphate carboxylase/oxygenase activate in rice, and leginsulin-binding protein in soybean have functions in the signal transduction pathway. Proteomics is well suited not only to determine interaction between pairs of proteins, but also to identify multisubunit complexes. Currently, a protein-protein interaction database for plant proteins (http://genome .c .kanazawa-u.ac.jp/Y2H)could be a very useful tool for the plant research community. Recently, we are separated proteins from grain filling and seed maturation in rice to perform ESI-Q-TOF/MS and MALDI-TOF/MS. This experiment shows a possibility to easily and rapidly identify a number of 2-DE separated proteins of rice by ESI-Q-TOF/MS and MALDI-TOF/MS. Therefore, the Information thus obtained from the plant proteome would be helpful in predicting the function of the unknown proteins and would be useful in the plant molecular breeding. Also, information from our study could provide a venue to plant breeder and molecular biologist to design their research strategies precisely.