• Journal of Microbiology and Biotechnology
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• v.26 no.11
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• pp.1993-2005
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• 2016

Bacillus pumilus is one of the most characterized microorganisms that are used for high-level production of select industrial enzymes. A novel B. pumilus SCU11 strain possessing high alkaline protease activity was obtained in our previous work. The culture supernatant of this strain showed efficient dehairing capability with minimal collagen damage, indicating promising potential applications in the leather industry. In this study, the strain's extracellular proteome was identified by LC-MS/MS-based shotgun proteomic analysis, and their related secretory pathways were characterized by BLAST searches. A total of 513 proteins, including 100 actual secreted and 413 intracellular proteins, were detected in the extracellular proteome. The functions of these secreted proteins were elucidated and four complete secretory systems (Sec, Tat, Com, and ABC transporter) were proposed for B. pumilus. These data provide B. pumilus a comprehensive extracellular proteome profile, which is a valuable theoretical and applicative basis for future genetic modifications and development of industrial enzymes.

• Korean Journal of Veterinary Research
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• v.50 no.4
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• pp.285-295
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• 2010

Protein expression patterns in Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) strains with diverse phenotypes, such as phage type, antibiotic resistance pattern and plasmid profiles were examined. For detailed analysis of proteins expressed by different S. Typhimurium strains, protein fractions were divided into detergent-rich phase (DP) and aqueous phase (AP) using triton X-114 detergent. The two phases were subjected to two-dimensional gel electrophoresis (2-DE), followed by protein identification using peptide mass fingerprinting (PMF). In the results, PMF showed that DP fractions consisted mainly of outer membrane proteins, whereas the AP fractions included cytosolic proteins. Comparison of 2-DE profiles of DP did not show any distinct protein spots which could be correlated with phage type, antibiotic resistance pattern or plasmid profile. However, comparisons of 2-DE profiles of the AP revealed differences in the protein spots, which could be correlated with the plasmid profile and phage types. Among these protein spots, flagellin was specific for strains containing a 90 kb plasmid. Compared to DT193 phage type, three protein spots in the range of pI 5.0-5.5 and MW 8-15 kDa of AP 2-DE profiles were absent in the DT104 phage types. Additionally, a protein spot with PI in the range of 4.5-5.0 and molecular weight (MW) between 51-69 kDa was specific for phage type DT104, while a protein spot with pI in the range of 4.0-4.8 and MW between 18-20 kDa was specific for DT193 phage type. These protein spots may be useful for discriminating phage types of S. Typhimurium.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.131-131
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• 2017

Though the Platycodon grandiflorum, has a broad range of pharmacologic properties, but the mechanisms underlying these effects remain unclear. In order to profile proteins from the nodal segment, callus, root and shoot, high throughput proteome approach was executed in the present study. Two-dimensional gels stained with CBB, a total of 84 differential expressed proteins were confirmed out of 839 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 58 differential expressed protein spots (${\geq}2-fold$) were analyzed using MASCOT search engine according to the similarity of sequences with previously characterized proteins along with the UniProt database. Out of 58 differential expressed protein, 32 protein spots were up-regulated such as ribulose-1,5-bisphosphate carboxylase, endoplasmic oxidoreductin-1, heat stress transcription factor A3, RNA pseudourine synthase 4, cysteine proteinase, GntR family transcriptional regulator, E3 xyloglucan 6-xylosyltransferase, while 26 differential protein spots were down-regulated such as L-ascorbate oxidase precursor, late embryogenesis abundant protein D-34, putative SCO1 protein, oxygen-evolving enhancer protein 3. However, the frequency distribution of identified proteins using iProClass databases, and assignment by function based on gene ontology revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding (17%), transferase activity (14%) and ion binding (12%). Taken together, the protein profile may provide insight clues for better understanding the characteristics of proteins and its metabolic activities in various explants of this essential medicinal plant P. grandiflorum.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.132-132
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• 2017

Plants, including Platycodon grandiflorum have been used globally across varied cultures as a safe natural source of medicines. From time immemorial, humans have relied on plants that could meet their basic necessities such as food, shelter, fuel and health. This study was executed to profile proteins from the hormone induced diploid and tetraploid roots using high throughput proteome approach. Two dimensional gels stained with CBB, a total of 64 differential expressed proteins were identified from the diploid root using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 20 differential expressed protein spots ( ${\geq}1.5-fold$) were analyzed using LTQ-FTICR MS whereas a total of 13 protein spots were up regulated and 7 protein spots were down-regulated. However, in the case of tetraploid root, a total of 78 differential expressed proteins were identified from tetraploid root of which a total of 28 differential expressed protein spots (${\geq}1.5-fold$) were analyzed by mass spectrometry whereas a total of 16 protein spots were up regulated and a total of 12 protein spots were down-regulated. However, proteins identified using iProClass databases revealed that the identified proteins from the explants were mainly associated with the nucleic acid binding, oxidoreductase activity, transporter activity and isomers activity. The exclusive protein profile may provide insight clues for better understanding the characteristics of protein function and its metabolic activity that can help for the development of the nutritional and breeding aspects of this economically important medicinal plant.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.125-125
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• 2017

The roots of Platycodon grandiflorum are commonly used for treating bronchitis, asthma, tuberculosis, diabetes, and other inflammatory diseases. Since the molecular mechanism underlying the roots of the plant is unclear. Therefore, the present study was conducted to profile proteins from liquid cultured tetraploid roots of Platycodon grandi orum fl using high throughput proteome approach. Two-dimensional gels stained with CBB, a total of 659 differentially expressed proteins were identified from the liquid medium cultured tetraploid roots of which 32 proteins spots (${\geq}1.5-fold$) were sorted for mass spectrometry analysis. Out of these 32 proteins, a total of 15 proteins were up-regulated such as Serine carboxypeptidase-like 27, Transcription factor bHLH150, 60 kDa jasmonate-induced protein, Cytosolic Fe-S cluster assembly factor NBP35, Regulatory associated protein of TOR 2 and a total of 17 proteins were down-regulated such as Protein G1-like2, Phenylalanine ammonia-lyase, Fructokinase-2, Trihelix transcription factor GT-3a, Guanine nucleotide-binding protein alpha-1 subunit. However, the frequency distribution of identified proteins was carried out within functional categories based on molecular functions, cellular components, and biological processes. Functional categorization revealed that the most of the identified proteins from the explants were mainly associated with the nucleic acid binding, oxidoreductase, transferase activity, protein binding and hydrolase activity. In addition, the proteomic feedback of tetraploid roots of P. grandiflorum may potentially be used to understand the characteristics of proteins and their functions.

• ALGAE
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• v.31 no.4
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• pp.379-390
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• 2016

When a multinucleate cell of Bryopsis plumosa was collapsed by a physical wounding, the extruded protoplasm aggregated into numerous protoplasmic masses in sea water. A polysaccharide envelope which initially covered the protoplasmic mass was peeled off when a cell membrane developed on the surface of protoplast in 12 h after the wounding. Transmission electron microscopy showed that the protoplasmic mass began to form a continuous cell membrane at 6 h after the wounding. The newly generated cell membrane repeated collapse and rebuilding process several times until cell wall developed on the surface. Golgi bodies with numerous vesicles accumulated at the peripheral region of the rebuilding cell at 24 h after the wounding when the cell wall began to develop. Several layers of cell wall with distinctive electron density developed within 48-72 h after the wounding. Proteome profile changed dramatically at each stage of cell rebuilding process. Most proteins, which were up-regulated during the early stage of cell rebuilding disappeared or reduced significantly by 24-48 h. About 70-80% of protein spots detected at 48 h after the wounding were newly appeared ones. The expression pattern of 29 representative proteins was analyzed and the internal amino acid sequences were obtained using mass spectrometry. Our results showed that a massive shift of gene expression occurs during the cell-rebuilding process of B. plumosa.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.57 no.2
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• pp.171-181
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• 2012

Lysine is the first limiting essential amino acid in cereals for humans and monogastric animals, although its content is generally low. A chemically induced high-lysine barley mutant, M98, has an agronomically undesirable shrunken endosperm trait. In order to obtain detailed insight into the atypical traits of M98 grains, we characterized amino acid composition and protein profiles of M98 and its parent cultivar Chalssalbori. Among a total of 16 amino acids, the percentage of each of the 7 amino acids, including lysine, was 1.2~1.8 times higher in M98, comparing to Chalssalbori. The percentage of proline and its precursor, glutamic acid, in M98 was about the half of that of the amino acids in Chalssalbori, but arginine synthesized from glutamic acid was 1.8 times higher in M98, compared that in the parent cultivar. Theses results indicated that the mutation in M98 grains might alter the proportion of amino acids linked to each other in a biosynthetic pathway. A comparison of grain proteome profiles between Chalssalbori and M98 revealed 70 differentially expressed protein spots, where 45 protein spots were up-regulated and 25 protein spots down-regulated in M98 compared to those in Chalssalbori. Of these changed protein spots, 53 were identified using nano-electrospray ionization liquid chromatography mass spectrometry. Most of these identified proteins were involved in various biological processes. In particular, 28 protein spots such as ${\beta}$-amylase, serpins and B3-hordein were identified as proteins associated with the atypical traits of M98. It was thought that a genetic study on the unique protein profile of M98 would be needed to develop an agronomically feasible barley cultivar with high-lysine trait.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.11
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• pp.1599-1607
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• 2004

This study examined the effects of pre-slaughter fasting, chasing stress and chiller ageing on objective meat quality, and their relations to the proteome profile of longissimus muscle using 20 male Korean native black pigs. Treatments were composed of two levels of pre-slaughter feed withdrawal, two levels of pre-slaughter stress and four chiller ageing times. A 15 min chasing stress immediately prior to slaughter significantly (p<0.05) decreased detectable levels of $\mu$-calpain activity during rigor development and chiller ageing, but did not have any direct effect on objective meat quality. On the other hand, pigs fed until the morning of slaughter resulted in significantly (p<0.05) higher hunter L* value and cooking loss than those which received an 18 h feed withdrawal prior to slaughter. Cooking loss and hunter L* value were constant during 7 d of chiller ageing, followed by significant increases at 14 d. The fed animals showed a significantly (p<0.05) higher hunter a* value at both 3 and 7 d, while the other group maintained a stable redness for 7 d. WB-shear force was not affected by the pre-slaughter treatments, but had significant (p<0.05) linear reduction from 1 to 7 d. A gelbased proteome analysis was performed on selected animals for low and high hunter L* values at 1 d. Ten and five spots had greater than two-fold spot densities for the low and high hunter L* groups, respectively. The ten spots included chain A, deoxyribounclease I complex with actin, heat shock protein 27 kDa, a protein similar to cardiac $Ca^{2+}$ release channel, and myosin heavy chain, while the five spots included chain A aldehyde dehydrogenase, glycerol-3 phosphate dehydrogenase, and hemoglobin alpha chain. In general, feeding until the morning of slaughter resulted in more desirable meat color, but appeared to reduce palatability due to increased cooking loss. Proteome analysis demonstrated that various proteins were concomitantly involved in the determination of final meat color. The most noticeable observation in the current study was that various isoforms for a particular protein differed in degradation and/or expression rate depending on meat quality.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.4
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• pp.1667-1674
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• 2012

Objective: To explore the differential protein expression profile in EC304 gastric cancer cells induced by alphastatin. Methods: Cultured EC304 cells in the exponential phase of growth were randomly divided into alphastatin and control groups. Total proteins were extracted and the two dimensional electrophoresis (2-DE) technique was applied to analyze differences in expression with ImageMaster 2D Platinum 5.0 software. Proteins were identified using the MASCOT database and selected differently expressed proteins were characterised by western blotting and immunofluorescence. Results: $1350{\pm}90$ protein spots were detected by the ImageMaster software in the 2-DE gel images from the control and alphastatin groups. The match rate was about 72-80% for the spectrum profiles, with 29 significantly different protein spots being identified, 10 upregulated, 16 downregulated, two new and one lost. The MASCOT search scores were 64-666 and the peptide matching numbers were 3-27 with sequence coverage of 8-62%. Twenty-three proteins were checked by mass spectrometry, including decrease in Nm23 and profilin-2 isoform b associated with the regulation of actin multimerisation induced by extracellular signals. Conclusion: The proteome in EC304 cells is dramatically altered by alphastatin, which appears to play an important role in modulating cellular activity and anti-angiogenesis by regulating protein expression and signal transduction pathways through Nm23 and profilin-2 isoform b, providing new research directions for anti-angiogenic therapy of gastric cancer.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.123-123
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• 2017

In spite of the potential medicinal significance and a wide range of pharmacologic properties of Platycodon grandiflorum, the molecular mechanism of its roots is still unknown. The present study was conducted to profile proteins from 3, 4 and 5 months aged diploid and tetraploid roots of Platycodon grandiflorum using high throughput proteome approach. Two-dimensional gels stained with CBB, a total of 68 differential expressed proteins were identified from the diploid root out of 767 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 29 differential expressed protein spots (${\geq}2-fold$) were analyzed using LTQ-FTICR MS whereas a total of 24 protein spots were up-regulated and 5 protein spots were down-regulated. On the contrary, in the case of tetraploid root, a total of 86 differential expressed proteins were identified from tetraploid root out of 1033 protein spots of which a total of 39 differential expressed protein spots (${\geq}2-fold$) were analyzed using LTQ-FTICR MS whereas a total of 21 protein spots were up-regulated and a total of 18 protein spots were down-regulated. It was revealed that the identified proteins from the explants were mainly associated with the nucleotide binding, oxidoreductase activity, transferase activity. Taken together, the identified proteins may be helpful to identify key candidate proteins for genetic improvement of plants.