• Journal of Microbiology and Biotechnology
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• 제16권5호
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• pp.799-803
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• 2006

It was reported that an accumulation of Sadenosyl-L-methionine increases production of actinorhodin in Streptomyces lividans and induces antibiotic biosynthetic genes. We also obtained the same result in Streptomyces coelicolor A3(2). Therefore, in order to identify proteins changed by the addition of S-adenosyl-L-methionine in S. coelicolor A3(2), LC/MS/MS analyses were carried out. Thirteen proteins that were not observed in the control were found.

• Genomics & Informatics
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• 제7권2호
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• pp.131-135
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• 2009

Domains are the building blocks of proteins. Exon shuffling is an important mechanism accounting for combination of a limited repertoire of protein domains in the evolution of multicellular species. A relative excess of domains encoded by symmetric exons in metazoan phyla has been presented as evidence of exon shuffling, and symmetric domains can be divided into old and new domains by determining the ages of the domains. In this report, we compare the spread, versatility, and subcellular localization of old and new domains by analyzing eight metazoan genomes and their respective annotated proteomes. We found that new domains have been expanding as multicellular organisms evolved, and this expansion was principally because of increases in class 1-1 domains amongst several classes of domain families. We also found that younger domains have been expanding in membranes and secreted proteins along with multi-cellular organism evolution. In contrast, old domains are located mainly in nuclear and cytoplasmic proteins. We conclude that the increasing mobility and versatility of new domains, in contrast to old domains, plays a significant role in metazoan evolution, facilitating the creation of secreted and transmembrane multidomain proteins unique to metazoa.

• Journal of Microbiology and Biotechnology
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• 제22권5호
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• pp.654-658
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• 2012

Osteoarthritis (OA) is the most common rheumatic pathology. One of the major objectives of OA research is the development of early diagnostic strategies such as those using proteomic technology. Synovial fluid (SF) in OA patients is a potential source of biomarkers for OA. The efficient and reliable preparation of SF proteomes is a critical step towards biomarker discovery. In this study, we have optimized a pretreatment method for twodimensional gel electrophoresis (2DE) separation of the SF proteome, by enriching low-abundance proteins and simultaneously removing hyaluronic acid, albumin, and IgG. SF samples pretreated using this optimized method were then evaluated by 1DE and 2DE separation followed by immunodetection of cartilage oligomeric matrix protein (COMP), a known OA biomarker, and by the identification of 3 proteins (apolipoprotein, haptoglobin precursor, and fibrinogen D fragment) that are related to joint diseases.

• Interdisciplinary Bio Central
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• 제5권1호
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• pp.2.1-2.3
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• 2013

Birth and development of information biology are introduced with its definition and scientific basis. The discipline lives on the two types of nutrition, one is a huge amount of biological data on genomes, gene expressions, proteomes, protein 3D structures, protein networks, and so forth. The other is the method of using them on a computer. The scientific basis of the two is evolution. To collect genome and gene expression data form laboratories in the world, annotate and dissimilate back to researchers worldwide, they built the EMBL database in Europe in 1982, GenBank in USA in 1984 and DNA Data Bank of Japan in 1987. On the other hand, the methods of using and analyzing those data have accordingly been developed. The two aspects advance the discipline further and further.

• Mass Spectrometry Letters
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• 제12권3호
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• pp.76-80
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• 2021

Scrub typhus is an acute febrile disease caused by the pathogenic bacterium Orientia tsutsugamushi, belonging to the Rickettsiaceae family. The shotgun proteomic analysis was performed using the sera of scrub typhus patients to identify the proteins having their origin in O. tsutsugamushi. Three different databases approaches were used for the identification of the proteomes. We identified the RsmD, an RNA methyltransferase as the commonly detected protein from all three approaches. This protein was not detected in the sera of healthy negative controls. We believe that this protein is a potential biomarker of Orientia tsutsugamushi present in the sera of scrub typhus patients.

• 한국미생물·생명공학회지
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• 제49권4호
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• pp.478-484
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• 2021

Cellular resources including transcriptional and translational machineries in bacteria are limited, yet microorganisms depend upon them to maximize cellular fitness. Bacteria have evolved strategies for using resources economically. Regulatory networks for the gene expression system enable the cell to synthesize proteins only when necessary. At the same time, regulatory interactions enable the cell to limit losses when the system cannot make a cellular profit due to fake substrates. Also, the architecture of the gene expression flow can be advantageous for clustering functionally related products, thus resulting in effective interactions among molecules. In addition, cellular systems modulate the investment of proteomes, depending upon nutrient qualities, and fast-growing cells spend more resources on the synthesis of ribosomes, whereas nonribosomal proteins are synthesized in nutrient-limited conditions. A deeper understanding of cellular mechanisms underlying the optimal allocation of cellular resources can be used for biotechnological purposes, such as designing complex genetic circuits and constructing microbial cell factories.

• Journal of Microbiology and Biotechnology
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• 제18권4호
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• pp.648-657
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• 2008

In this study, we used functional genomic strategies, proteomics and quantitative real-time (qRT)-PCR, to advance our understanding of genes associated with fumonisin production in the fungus Fusarium verticillioides. Earlier studies have demonstrated that deletion of the FCC1 gene, which encodes a C-type cyclin, leads to a drastic reduction in fumonisin production and conidiation in the mutant strain (FT536). The premise of our research was that comparative analysis of F. verticillioides wild-type and FT536 proteomes will reveal putative proteins, and ultimately corresponding genes, that are important for fumonisin biosynthesis. We isolated proteins that were significantly upregulated in either the wild type or FT536 via two-dimensional polyacrylamide gel electrophoresis, and subsequently obtained sequences by mass spectrometry. Homologs of identified proteins, e.g., carboxypeptidase, laccase, and nitrogen metabolite repression protein, are known to have functions involved in fungal secondary metabolism and development. We also identified gene sequences corresponding to the selected proteins and investigated their transcriptional profiles via quantitative real-time (qRT)-PCR in order to identify genes that show concomitant expression patterns during fumonisin biosynthesis. These genes can be selected as targets for functional analysis to further verify their roles in $FB_1$ biosynthesis.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2001년도 추계학술발표대회
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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.

• Molecular & Cellular Toxicology
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• 제1권1호
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• pp.32-39
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• 2005

Polycyclic aromatic hydrocarbons (PAHs) are an important class of environmentally prevalent xenobiotics that exert complex effects on the biological system and characterized as probably carcinogenic materials. Single cell gel electrophoresis assays were performed in order to evaluate DNA damage occurring in the T-and B lymphocytes, spleens (T/B-cell), bone marrow, and livers of mouse exposed to mixture of PAHs (Benzo(a)pyrene, Benzo(e)pyrene, Fluoranthene, Pyrene) at dose of 400, 800, or 1600 mg/kg body weight for 2 days. DNA damage of the cells purified from mice was increased in dose dependent manner. In the blood cells and organs, DNA damage was also discovered to vary directly with PAHs. Especially T-cells had been damaged more than B-cell. Plasma proteomes were separated by 2-dimensional electrophoresis with pH 4-7 ranges of IPG Dry strips and many proteins showed significant up-and -down expressions with the dose dependent manner. Of these, significant 4 spots were identified using matrix-assisted laser desorption/ionization-time of fight (MALDI-TOF) mass spectrometry. Identified proteins were related to energy metabolism and signal transduction.

• Bulletin of the Korean Chemical Society
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• 제35권3호
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• pp.933-937
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• 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.