• Korean Journal of Microbiology
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• v.53 no.3
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• pp.163-169
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• 2017

Strains D4 and D5 were isolated from peach-rotten soil during the peach harvest season. The isolates were identified based on morphological and biochemical characterization, and identification was determined by 16S rRNA gene sequencing. Results showed that D4 has high similarity to Lactobacillus plantarum ATCC $14917^T$ and Lactobacillus pentosus ATCC $8041^T$ at 99.05% and 98.98%, respectively. D5 was also similar to Lactobacillus pentosus ATCC $8041^T$ and Lactobacillus plantarum ATCC $14917^T$ at 98.71% and 98.64%, respectively. In contrast, isolates showed differences in carbohydrate utilization in comparison to Lactobacillus plantarum ATCC $14917^T$ and Lactobacillus pentosus ATCC $8041^T$. In view of this we performed VITEK MS matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis, multiplex PCR fingerprinting, and random amplified polymorphic DNA (RAPD)-PCR to further confirm the identification of D4 and D5. The results of these analyses showed that both strains were most similar to Lactobacillus plantarum.

• BMB Reports
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• v.38 no.6
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• pp.650-660
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• 2005

Proteins accumulated in dry, stratified Arabidopsis seeds or young seedlings, totaled 1100 to 1300 depending on the time of sampling, were analyzed by using immobilized pH gradient 2-DE gel electrophoresis. The molecular identities of 437 polypeptides, encoded by 355 independent genes, were determined by MALDI-TOF or TOF-TOF mass spectrometry. In the sum, 293 were present at all stages and 95 were accumulated during the time of radicle protrusion while another 18 appeared in later stages. Further analysis showed that 226 of the identified polypeptides could be located in different metabolic pathways. Proteins involved in carbohydrate, energy and amino acid metabolism constituted to about 1/4, and those involved in metabolism of vitamins and cofactors constituted for about 3% of the total signal intensity in gels prepared from 72 h seedlings. Enzymes related to genetic information processing increased very quickly during early imbibition and reached highest level around 30 h of germination.

• Korean Journal of Environmental Agriculture
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• v.32 no.1
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• pp.48-54
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• 2013

BACKGROUND: Sorghum (Sorghum bicolor (L.) Moench) ranks as the 6th most planted crop in the world behind wheat, rice, maize, soybean, and barley. The objective of this study was to identify bio-marker among sorghum cultivars using proteomics approach such as two-dimensional polyacrylamide gel electrophoresis (2-DE) coupled with mass spectrometry (MS). METHODS AND RESULTS: Proteins were extracted from sorghum seed, and separated by 2-DE. Total 652 spots were detected from 4 different sorghum seed after staining of 2-DE with colloidal Coomassie brilliant blue (CBB). Among them, 8 spots were differentially expressed and were identified using MALDI-TOF/TOF mass spectrometry. They were involved in RNA metabolism (spot1, spot 4), heat shock proteins (HSPs, spot 2), storage proteins (spot 3, spot 5, and spot 6), and redox related proteins (spot 8). Eight of these proteins were highly up-regulated in Whinchalsusu (WCS). The HSPs, Cupin family protein, and Globulin were specifically accumulated in WCS. The DEAD-box helicase was expressed in 3 cultivars except for WCS. Ribonuclease T2 and aldo-keto reductase were only expressed in 3 cultivars except for Daepung-susu (DPS). CONCLUSION(S): Functions of identified proteins were mainly involved in RNA metabolism, heat shock protein (HSP), and redox related protein. Thus, they may provide new insight into a better understanding of the charactreization between the cultivars of sorghum.

• Journal of Microbiology and Biotechnology
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• v.16 no.1
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• pp.25-31
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• 2006

Changes of CP4 5-enolpyruvylshikimate-3-phosphate synthase (CP4 EPSPS) in the glyphosate-tolerant Roundup Ready soybean were examined using purified CP4 EPSPS produced in cloned Escherichia coli as a control. CP4 EPSPS in genetically modified soybean was detected by twodimensional gel electrophoresis (2-DE) and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and electrospray ionization tandem mass spectrometry (ESI-MS/MS) with databases. CP4 EPSPS in soybean products was resolved on 2-DE by first isoelectric focusing (IEF) based on its characteristic pI of 5.1, followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) based on its molecular mass of 47.5 kDa. We quantified various percentages of soybean CP4 EPSPS. The quantitative analysis was performed using a 2D software program on artificial gels with spots varying in Gaussian volumes. These results suggested that 2-DE image analysis could be used for quantitative detection of GM soybean, unlike Western blotting.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.4
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• pp.1663-1666
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• 2012

Background and Objective: Protein expression in colon and rectal cancer (CRC) and paired normal tissues was examined by two-dimensional gel electrophoresis (2-DE) to identify differentially expressed proteins. Materials and Methods: Five fresh colorectal cancer and paired adjacent normal tissues were obtained and differentially expressed protein spots were determined using PDQuest software, with identification on the basis of MALDI-TOF mass spectra. Results: Compared with normal colorectal mucosa, protein abnormal expression of 65 spots varying more than 1.5 times were found in 2-DE gels from colorectal cancer samples (P<0.05); forty-two proteins were up-regulated and 23 were down-regulated; twelve protein spots were identified using mass spectrometry, of which 8 were up-regulated, includimng HSPB1and Annexin A4, while 4 were down-regulated, the results being consistent with Western blot findings. Conclusions: Two-dimensional electrophoresis reference maps for CRC tissues and adjacent normal mucosa (NMC) were established and 12 differentially expressed proteins were identified. Up-regulated HSPB1 and Annexin A4 may play many important roles in the pathogenesis of colorectal cancer.

• Proceedings of the Korean Society of Sericultural Science Conference
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• 2003.04a
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• pp.75-75
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• 2003

We have purified and characterized cecropin A-like antibacterial peptide from the hemolymph of immunized Galleria mellonella larvae. Acid extraction, gel filtration, preparative acid urea PAGE, and reversed-phase HPLC were used for purification of peptide. The molecular mass of the purified peptide was estimated to be 4160.68 Da by MALDI-TOF mass spectrometry. (omitted)

• Journal of Microbiology and Biotechnology
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• v.21 no.6
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• pp.574-581
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• 2011

A Gram-positive bacterium was isolated from the saline soils of Jangpura (U.P.), India, and showed high-level of radiation-resistant property and survived upto 12.5 kGy dose of gamma radiation. The 16S rDNA sequence of this strain was examined, identified as Bacillus sp. strain HKG 112, and was submitted to the NCBI GenBank (Accession No. GQ925432). The mechanism of radiation resistance and gene level expression were examined by proteomic analysis of whole-cell extract. Two proteins, 38 kDa and 86.5 kDa excised from SDS-PAGE, which showed more significant changes after radiation exposure, were identified by MALDI-TOF as being flagellin and S-layer protein, respectively. Twenty selected 2-DE protein spots from the crude extracts of Bacillus sp. HKG 112, excised from 2- DE, were identified by liquid chromatography mass spectrometry (LC-MS) out of which 16 spots showed significant changes after radiation exposure and might be responsible for the radiation resistance property. Our results suggest that the different responses of some genes under radiation for the expression of radiation-dependent proteins could contribute to a physiological advantage and would be a significant initial step towards a fullsystem understanding of the radiation stress protection mechanisms of bacteria in different environments.

• The Korean Journal of Mycology
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• v.36 no.2
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• pp.183-188
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• 2008

A fibrinolytic serine protease was purified from the fruiting bodies of an edible mushroom, Albatrellus confluens. The enzyme had a molecular mass of 30086.41 Da, as measured by MALDI-TOF mass spectrometry. The N-terminal amino acid sequence of the enzyme was Glu-Thr-Val-Thr-Glu-Thr-Thr-Ala -Pro-Trp-Gly-Leu-Ser-Arg-Ile. It displayed optimal activity at $50^{\circ}C$ and within a pH range of $8.0{\sim}10.0$, suggesting that the enzyme is an alkaline protease. The enzyme was stable up to $30^{\circ}C$. The enzyme displayed a strong substrate specificity for the synthetic peptide, N-Suc-Ala-Ala-Pro-Phe pNA. The enzyme activity was completely inhibited by addition of PMSF, indicating that the enzyme is a serine protease. No inhibition was observed following addition of E-64, pepstatin, or EDTA. The activity of the purified enzyme was decreased in the presence $Fe^{2+}$ or $Co^{2+}$, and the enzyme was completely inhibited by addition of $Hg^{2+}$. From these results, we propose that Albatrellus confluens could be used for biofunctional foods development and has potential therapeutic value for the treatment of vascular diseases.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.7
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• pp.922-926
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• 2005

The present study was aimed to investigate proteome affected by Panax ginseng extracts in chicken muscles. The whole muscle proteins from chicken fed boiled extracts of 0% (control), 1%, 3%, and 5% Panax ginseng in water were separated by two-dimensional electrophoresis (2-DE) gels using immobilized non-linear gradient (pH 3-10) strips. More than 300 protein spots were detected on silver staining gels. Among them, four protein spots were distinctively up-regulated by Panax ginseng treatments and further investigated by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The obtained MS data were searched against SwissProt database using the Mascot search engine. The up-regulated proteins were finally identified as $\alpha$-tropomyosin (2 spots), triosephosphate isomerase, and one unknown protein. Based on the known functions of the identified proteins, they are highly related to muscle development and enhanced immunity in chickens. These proteins can give valuable information of biochemical roles for Panax ginseng in chicken meats.

• Environmental Mutagens and Carcinogens
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• v.22 no.4
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• pp.236-242
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• 2002

Using agarose-coupled methotrexate, we have successfully isolated two proteins, which have strong interactions with methotrexate. The two proteins were analyzed by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry and identified as carbamoyl-phosphate synthetase 2 and phosphoribosylglycinamide formyltransferase, respectively. Interestingly, both of these two proteins are essential key enzymes in nucleotide biosynthetic pathways, like dihydrofolate reductase, a well-known methotrexate target. We confirmed the specificity of their interactions between methotrexate and two target proteins by the methods of competition binding assay, which were followed by western blotting using antibody against carbamoyl-phosphate synthetase 2 and phosphoribosylglycinamide formyltransferase, respectively. Moreover, we could observe that carbamoyl-phosphate synthetase 2 is overexpressed in methotrexate-resistant MOLT-3 cells comparing with control MOLT-3 cells. This result indicates that carbamoyl-phosphate synthetase 2 may be a novel target of methotrexate in cancer therapy. We propose that chemical proteomics can be a powerful technique to identify target proteins of a chemical.