• KOREAN JOURNAL OF CROP SCIENCE
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• v.54 no.3
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• pp.332-338
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• 2009

Rapid extension of genomic database leads to the remarkable advance of functional genomics. This study proposes a novel methodology of functional analysis using 5-methyltrytophan (5 MT) mutant together with their 2-DE analysis and public microarray database. A total of 24 proteins was changed in 5 MT mutant and four remarkably different expressed proteins were identified. Among them, three spots were converted to Affymetrix probe. A total of 155 microarray samples from Gene Expression Omnibus (GEO) in NCBI was retrieved and followed by constructing gene co-expression networks over a broad range of biological issues through Self-Organising Tree Algorithm. Three co-expressing gene clusters were retrieved and each functional categorization with differential expression pattern was exhibited from 5 MT resistance mutant rice. It was indicated new co-expression networks in the mutant. This study suggests that on investigating possibility which correspond 2-DE to microarray database with their full potential.

• 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.16 no.6
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• pp.911-920
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• 2006

[ $CD8^+$ ] T Iymphocytes with the cytotoxic activity and capability to release various cytokines are the major players in immune responses against viral infection and cancer. To identify the proteins specific to resting or activated human CD8$^+$ T cells, human CD8$^+$ T cells were activated with anti-CD3+anti-CD28 mAb in the presence of IL-2. The solubilized proteins from resting and activated human CD8$^+$ T cells were separated by high-resolution two-dimensional polyacrylamide gel electrophoresis, and their proteomes were analyzed. Proteomic analysis of resting and activated T cells resulted in identification of 35 proteins with the altered expression. Mass spectrometry coupled with Profound and SWISS-PROT database analysis revealed that these identified proteins are to be functionally associated with cell proliferation, metabolic pathways, antigen presentation, and intracellular signal transduction pathways. We also identified six unknown proteins predicted from genomic DNA sequences specific to resting or activated CD8$^+$ T cells. Protein network studies and functional characterization of these novel proteins may provide new insight into the signaling transduction pathway of CD8$^+$ T cell activation.

• Journal of Microbiology and Biotechnology
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• v.25 no.2
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• pp.288-295
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• 2015

Salmonella enterica serovar Enteritidis is the predominant agent causing salmonellosis in chickens and other domestic animals. In an attempt to identify antigenic S. Enteritidis outer membrane proteins (OMPs) that may be useful for subunit vaccine development, we established a proteomic map and database of antigenic S. Enteritidis OMPs. In total, 351 and 301 spots respectively from S. Enteritidis strain 270 and strain 350 were detected by two-dimensional gel electrophoresis. Fifty-one antigen-reactive spots were detected by antisera on two-dimensional immunoblots and identified as 12 specific proteins by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. OmpA and DNA starvation/stationary phase protection protein (Dps) were the most abundant proteins among the identified OMPs, comprising 22 and 12 protein species, respectively. Interestingly, we found that the Dps of S. Enteritidis is also antigenic. OmpW was also verified to have high antigenicity. These results show that OmpA, Dps, and possibly OmpW are antigenic proteins. This study provides new insights into our understanding of the immunogenic characteristics of S. Enteritidis OMPs.

• Parasites, Hosts and Diseases
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• v.48 no.3
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• pp.195-201
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• 2010

We studied on the proteomic characteristics of Toxoplasma gondii KI-1 tachyzoites which were originally isolated from a Korean patient, and compared with those of the well-known virulent RH strain using 2-dimensional electrophoresis (2-DE), mass spectrometry, and quantitative real-time PCR. Two-dimensional separation of the total proteins isolated from KI-1 tachyzoites revealed up to 150 spots, of which 121 were consistent with those of RH tachyzoites. Of the remaining 29 spots, 14 showed greater than 5-fold difference in density between the KI-1 and RH tachyzoites at a pH of 5.0-8.0. Among the 14 spots, 5 from the KI-1 isolate and 7 from the RH strain were identified using MALDI-TOF mass spectrometry and database searches. The spots from the KI-1 tachyzoties were dense granule proteins (GRA 2,3,6, and 7), hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGRPTase), and uracil phosphoribosyltransferase (UPRTase). The spots from the RH strain were surface antigen 1 (SAG 1), L-lactate dehydrogenase (LDH), actin, chorismate synthase, peroximal catalase, hexokinase, bifunctional dihydrofolate reductase-thymidylate synthase (DHTR-TS), and nucleosidetriphosphatases (NTPases). Quantitative real-time PCR supported our mass spectrometric results by showing the elevated expression of the genes encoding GRA 2,3, and 6 and UPRTase in the KI-1 tachyzoites and those encoding GRA 7, SAG 1, NTPase, and chorismate synthase in the RH tachyzoites. These observations demonstrate that the protein compositions of KI-1 and RH tachyzoites are similar but differential protein expression is involved in virulence.

• Journal of Ginseng Research
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• v.42 no.3
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• pp.343-351
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• 2018

Background: Red ginseng is a popularly used traditional medicine with antiaging effects in Asian countries. The present study aimed to explore the changes in protein expression underlying the mechanisms of life span extension and antiaging caused by red ginseng extract (RGE) in Drosophila melanogaster. Methods: A proteomic approach of two-dimensional polyacrylamide gel electrophoresis (2-DE) was used to identify the differential abundance of possible target proteins of RGE in D. melanogaster. The reliability of the 2-DE results was confirmed via Western blotting to measure the expression levels of selected proteins. Proteins altered at the expression level after RGE treatment (1 mg/mL) were identified by matrix-assisted laser desorption/ionization-time of flight tandem mass spectrometry and by searching against the National Center for Biotechnology nonredundant and Uniprot protein databases. The differentially expressed proteins were analyzed using bioinformatics methods. Results: The average survival life span of D. melanogaster was significantly extended by 12.60% with RGE treatment (1 mg/mL) compared to untreated flies. This followed increased superoxide dismutase level and decreased methane dicarboxylic aldehyde content. Based on the searching strategy, 23 differentially expressed proteins were identified (16 up-regulated and 7 down-regulated) in the RGE-treated D. melanogaster. Transduction pathways were identified using the Kyoto Encyclopedia of Genes and Genomes database, and included the hippo and oxidative phosphorylation pathways that play important roles in life span extension and antiaging process of D. melanogaster. Conclusion: Treatment with RGE in D. melanogaster demonstrated that mechanisms of life span extension and antiaging are regulated by multiple factors and complicated signal pathways.

• BMB Reports
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• v.37 no.1
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• pp.75-82
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• 2004

Recent years saw a dramatic increase in genomic and proteomic data in public archives. Now with the complete genome sequences of human and other species in hand, detailed analyses of the genome sequences will undoubtedly improve our understanding of biological systems and at the same time require sophisticated bioinformatic tools. Here we review what computational challenges are ahead and what are the new exciting developments in this exciting field.

• Journal of Plant Biotechnology
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• v.32 no.4
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• pp.251-256
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• 2005

Cytokinins are essential plant hormones that play crucial roles in various aspects of plant growth and development. To better understand the molecular mechanisms of cytokinin action, we identified cytokinin related proteins by a proteomic approach. Proteins extracted from control and trans-zeatin treated Arabidopsis seedlings were separated and analyzed by two dimensional gel analysis. Differentially expressed protein spots were identified with peptide mass fingerprinting based on matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and database searching, We obtained ten up-regulated and one down-regulated proteins upon t-zeatin treatment. The expression of the following proteins was induced; pollen allergen like protein, L-ascorbate peroxidase, tetrapyrrole methylase family protein, SGT1 protein homolog, disease resistance related protein, maternal embryogenesis control protein, paxneb related protein, gluthathione S-transferase and IAA amino acid hydrolase homolog.

• Plant Biotechnology Reports
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• v.4 no.4
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• pp.311-319
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• 2010

Lettuce is an economically important leafy vegetable that accumulates a milk-like sap called latex in the laticifer. Previously, we conducted a large-scale lettuce latex proteomic analysis. However, the identified proteins were obtained only from lettuce ESTs and proteins deposited in NCBI databases. To extend the number of known latex proteins, we carried out an analysis identifying 302 additional proteins that were matched to the NCBI non-redundant protein database. Interestingly, the newly identified proteins were not recovered from lettuce EST and protein databases, indicating the usefulness of this hetero system in MudPIT analysis. Gene ontology studies revealed that the newly identified latex proteins are involved in many processes, including many metabolic pathways, binding functions, stress responses, developmental processes, protein metabolism, transport and signal transduction. Application of the non-redundant plant protein database led to the identification of an increased number of latex proteins. These newly identified latex proteins provide a rich source of information for laticifer research.

• Journal of Microbiology and Biotechnology
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• v.22 no.6
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• pp.780-787
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• 2012

The maize pathogen Gibberella moniliformis produces fumonisins, a group of mycotoxins associated with several disorders in animals and humans, including cancer. The current focus of our research is to understand the regulatory mechanisms involved in fumonisin biosynthesis. In this study, we employed a proteomics approach to identify novel genes involved in the fumonisin biosynthesis under nitrogen stress. The combination of genome sequence, mutant strains, EST database, microarrays, and proteomics offers an opportunity to advance our understanding of this process. We investigated the response of the G. moniliformis proteome in limited nitrogen (N0, fumonisin-inducing) and excess nitrogen (N+, fumonisin-repressing) conditions by one- and two-dimensional electrophoresis. We selected 11 differentially expressed proteins, six from limited nitrogen conditions and five from excess nitrogen conditions, and determined the sequences by peptide mass fingerprinting and MS/MS spectrophotometry. Subsequently, we identified the EST sequences corresponding to the proteins and studied their expression profiles in different culture conditions. Through the comparative analysis of gene and protein expression data, we identified three candidate genes for functional analysis and our results provided valuable clues regarding the regulatory mechanisms of fumonisin biosynthesis.