• Environmental Analysis Health and Toxicology
• /
• v.29
• /
• pp.19.1-19.10
• /
• 2014

Objectives Lysosome is the cell-organelle which is commonly used as biomonitoring tool in environmental pollution. In this study, the lysosomal proteomic of the yeast Saccharomyces cerevisiae was analyzed for utilization in the detection of toxic substances in mine water samples. Methods This work informs the expression of lysosomal proteomic in yeast in response with toxic chemicals, such as sodium meta-arsenite and tetracycline, for screening specific biomarkers. After that, a recombinant yeast contained this biomarker were constructed for toxic detection in pure toxic chemicals and mine water samples. Results Each chemical had an optimal dose at which the fluorescent protein intensity reached the peak. In the case of water samples, the yeast showed the response with sample 1, 3, 4, and 5; whereas there is no response with sample 2, 6, and 7. Conclusions The recombinant yeast showed a high ability of toxic detection in response with several chemicals such as heavy metals and pharmaceuticals. In the case of mine water samples, the response varied depending on the sample content.

• Journal of Microbiology and Biotechnology
• /
• v.26 no.12
• /
• pp.2127-2137
• /
• 2016

A mangrove microbial community was analyzed at the gene and protein levels using metagenomic and proteomic methods with the green macroalgae Enteromorpha prolifera as the substrate. Total DNA was sequenced on the Illumina HiSeq 2000 PE-100 platform. Two-dimensional gel electrophoresis in combination with liquid chromatography tandem mass spectrometry was used for proteomic analysis. The metagenomic data revealed that the orders Pseudomonadales, Rhizobiales, and Sphingomonadales were the most prevalent in the mangrove microbial community. By monitoring changes at the functional level, proteomic analyses detected ATP synthase and transporter proteins, which were expressed mainly by members of the phyla Proteobacteria and Bacteroidetes. Members of the phylum Proteobacteria expressed a high number of sugar transporters and demonstrated specialized and efficient digestion of various glycans. A few glycoside hydrolases were detected in members of the phylum Firmicutes, which appeared to be the main cellulose-degrading bacteria. This is the first report of multiple "omics" analysis of E. prolifera degradation. These results support the fact that key enzymes of glycoside hydrolase family were expressed in large quantities, indicating the high metabolic activity of the community.

• 한국환경농학회:학술대회논문집
• /
• 2011.07a
• /
• pp.196-204
• /
• 2011

Abiotic stress is the primary cause of crop loss worldwide, reducing average yields for most major crop plants by more than 50%. In addition, future agricultural production and management will encounter multifaceted challenges from global climate change. Therefore, it is necessary to study the molecular response of crop plants to the stresses in order to develop appropriate strategies to sustain food production under adverse environmental conditions. We carried out a large scale proteomic analysis of soybean plants in response to various abiotic stresses, including drought, salinity, waterlogging and their interactions. Proteins were analyzed by two dimensional polyacrylamide gel electrophoresis followed by matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry. The identified proteins are involved in a wide range of cellular functions. In addition to the well known stress-associated proteins, we identified several novel proteins, which were not reported before. In many cases our proteomic data bridges the gap between mRNA and metabolite data. Our studie provides new insights into identification of abiotic stress responsive proteins in soybean, and demonstrates the advantages of proteomic analysis in dissecting metabolic and regulatory networks.

• Mycobiology
• /
• v.45 no.3
• /
• pp.226-231
• /
• 2017

Coprinopsis cinerea was employed to investigate the fungal response to gravity. Mycelium growth revealed a consistent growth pattern, irrespective of the direction of gravity (i.e., horizontal vs. perpendicular). However, the fruiting body grew in the direction opposite to that of gravity once the primordia had formed. For the proteomic analysis, only curved-stem samples were used. Fifty-one proteins were identified and classified into 13 groups according to function. The major functional groups were hydrolases and transferases (16%), signal transduction (15%), oxidoreductases and isomerases (11%), carbohydrate metabolism (9%), and transport (5%). To the best of our knowledge, this is the first report on a proteomic approach to evaluate the molecular response of C. cinerea to gravity.

• Korean Journal of Food Science and Technology
• /
• v.43 no.1
• /
• pp.12-16
• /
• 2011

This study was conducted to identify the differences in proteomic characteristics between Ca-enriched king oyster mushrooms and general king oyster mushrooms. A combined high-throughput proteomic approach was employed to determine the expression profiles and identity of proteins using 2-dimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. The overall distribution patterns of the proteins were quite similar, but many of the protein spot intensities varied. A total of 10 proteins, representing a significant difference in the quantities of protein betweenthe two types of mushrooms, were successfully identified. Among these proteins, eight kinds were increased in the Ca-enriched king oyster mushrooms and two kinds were decreased. This study showed that proteomic analysis can help define specific changes in protein level and composition, which can occur in mushrooms where Ca content may or may not be enriched.

• Journal of Plant Biotechnology
• /
• v.37 no.2
• /
• pp.196-204
• /
• 2010

With the completion of genome sequencing of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. The recent techniques of proteomics have been advanced quickly so that the high-throughput and systematic analyses of cellular proteins are enabled in combination with bioinformatics tools. Furthermore, the development of proteomic techniques helps to elucidate the functions of proteins under stress or diseased condition, resulting in the discovery of biomarkers responsible for the biological stimuli. Ultimate goal of proteomics orients toward the entire proteome of life, subcellular localization, biochemical activities, and their regulation. Comprehensive analysis strategies of proteomics can be classified as three categories: (i) protein separation by 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification by either Edman sequencing or mass spectrometry (MS), and (iii) quanitation of proteome. Currently MS-based proteomics turns shiftly from qualitative proteome analysis by 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, to quantitative proteome analysis. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. The in vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes, protein-labeling tagging with isotope-coded affinity tag, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope labeled amino acid can be in vivo labeled into live culture cells through metabolic incorporation. MS-based proteomics extends to detect the phosphopeptide mapping of biologically crucial protein known as one of post-translational modification. These complementary proteomic techniques contribute to not only the understanding of basic biological function but also the application to the applied sciences for industry.

• Bulletin of the Korean Chemical Society
• /
• v.35 no.3
• /
• pp.933-937
• /
• 2014

A derivative of Mycobacterium bovis Bacillus Calmette-Guerin (BCG) has been used for the preparation of tuberculosis vaccines. To establish a Korean tuberculosis vaccine derived from BCG-Pasteur $1173P_2$, genome sequencing of a BCG-Korea strain was completed by Joung and coworkers. A comparison analysis of the genome sequences of the BCG-Pasteur $1173P_2$ and BCG-Korea strains showed marginal increases in the total genome length (~0.05%) and the number of genes (~4%) in the BCG-Korea genome. However, how the genomic changes affect the BCG-Korea protein expression levels remains unknown. Here, we provide evidence of the proteomic alterations in the BCG-Korea strain by using a SWATH-based mass spectrometric approach (Sequential Window Acquisition of all THeoretical mass spectra). Twenty BCG proteins were selected by top-rank identification in the BCG proteome analysis and the proteins were quantified by the SWATH method. Thirteen of 20 proteins showing significant changes were enough to discriminate between the two BCG proteomes. The SWATH method is very straightforward and provides a promising approach owing to its strong reliability and reproducibility during the proteomic analysis.

• Food Science of Animal Resources
• /
• v.33 no.2
• /
• pp.281-286
• /
• 2013

Salmonella Gallinarum (SG) is known as an important pathogen that causes fowl typhoid in chickens. To investigate SG outer-membrane proteins (OMPs) as a vaccine candidate, we used proteomic mapping and database analysis techniques with extracted OMPs. Also, extracted OMPs were evaluated in several aspects to their safety, immune response in their host and protective effects. Our research has established a proteomic map and database of immunogenic SG-OMPs used as inactive vaccine against salmonellosis in chickens. A total of 22 spots were detected by 2-dimensional gel electrophoresis and immunogenic protein analysis. Eight spots were identified by Matrix-Assisted Laser Desorption/Ionization-Time of Flight-Mass spectrometry (MALDI-TOF-MS) and peptide mass fingerprinting (PMF) and categorized into four different types of proteins. Among these proteins, OmpA is considered to be an immunogenic protein and involved in the hosts' immune system. To estimate the minimum safety dose in chickens, 35 brown layers were immunized with various concentrations of OMPs, respectively. Consequently, all chickens immunized with more than a $50{\mu}g$ dose were protected against challenges. Moreover, intramuscular administration of OMPs to chickens was more effective compared to subcutaneous administration. These results suggest that the adjuvanted SG-OMP vaccine not only induces both the humoral and cellular immune response in the host but also highly protects the hosts' exposed to virulent SG with $50{\mu}g$ OMPs extracted by our method.

• BMB Reports
• /
• v.48 no.1
• /
• pp.19-24
• /
• 2015

A mouse homozygous for the spontaneous mutation uncovered (Uncv) has a hairless phenotype. A 309-bp non-frameshift deletion mutation in the N-terminal cytoplasmic domain of iRhom2 was identified in Uncv mice ($iRhom2^{Uncv}$) using target region sequencing. The detailed molecular basis for how the iRhom2 mutation causes the hairless phenotype observed in the homozygous $iRhom2^{Uncv}$ mouse remains unknown. To identify differentially expressed proteins in the skin of wild-type and homozygous $iRhom2^{Uncv}$ littermates at postnatal day 5, proteomic approaches, including two-dimensional gel electrophoresis and mass spectrometry were used. Twelve proteins were differentially expressed in the skin in a comparison between wild-type and homozygous $iRhom2^{Uncv}$ mice. A selection of the proteomic results were tested and verified using qRT-PCR, western blot and immunohistochemistry. These data indicate that differentially expressed proteins, especially KRT73, MEMO1 and Coro-1, might participate in the mechanism by which iRhom2 regulates the development of murine skin.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.8
• /
• pp.4093-4095
• /
• 2012

Objective: To determine whether pituitary adenomas can be diagnosed by identifying protein biomarkers in the serum. Methods: We compared serum proteins from 65 pituitary adenoma patients and 90 healthy donors using proteomic fingerprint technology combining magnetic beads with matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS). Results: A total of 42 M/Z peaks were identified as related to pituitary adenoma (P<0.01). A diagnostic model established based on three biomarkers (3382.0, 4601.9, 9191.2) showed that the sensitivity of diagnosing pituitary adenoma was 90.0% and the specificity was 88.3%. The model was further tested by blind analysis showing that the sensitivity was 88.0% and the specificity was 83.3%. Conclusions: These results suggest that proteomic fingerprint technology can be used to identify pituitary adenoma biomarkers and the model based on three biomarkers (3382.0, 4601.9, 9191.2) provides a powerful and reliable method for diagnosing pituitary adenoma.