• Journal of Microbiology and Biotechnology
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• 제21권4호
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• pp.421-429
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• 2011

For precise identification of a Lactobacillus K1 isolate, LC-MS/MS analysis of the putative surface layer protein was performed. The results obtained from LTQ-FT-ICR mass spectrometry confirmed that the analyzed protein spot is the surface layer protein originating from Lb. helveticus species. Moreover, the identified protein has the highest similarity with the surface layer protein from Lb. helveticus R0052. To evaluate the proteomic study, multilocus sequence analysis of selected housekeeping gene sequences was performed. Combination of 16S rRNA sequencing with partial sequences for the genes encoding the RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), translational elongation factor Tu (tuf), and Hsp60 chaperonins (groEL) also allowed to classify the analyzed isolate as Lb. helveticus. Further classification at the strain level was achieved by sequencing of the slp gene. This gene showed 99.8% identity with the corresponding slp gene of Lb. helveticus R0052, which is in good agreement with data obtained by nano-HPLC coupled to an LTQ-FT-ICR mass spectrometer. Finally, LC-MS/MS analysis of surface layer proteins extracted from three other Lactobacillus strains proved that the proposed method is the appropriate molecular tool for the identification of S-layer-possessing lactobacilli at the species and even strain levels.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.119-119
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• 2017

Growth related to morphological and proteome response under waterlogging stress in sorghum has not yet been elucidated. Understanding how plants respond to waterlogging, the present study was conducted in seedlings leaf of the Nam-pung chal cultivar. Regarding 3-leaf stage of sorghum, stem length and plant height were slightly decreased in the treatments during ten days of waterlogging, and chlorophyll contents were also significantly different from 7 days of waterlogging treatment. The results observed from the present study were considered to be influenced by the waterlogging stress more in the $5^{th}$ leaf stage of the growth period of the sorghum, and as the waterlogging treatment progressed, the waterlogging stress gradually influenced the growth difference between the control and the treatment respectively. Using 2-DE method, a total of 74 differentially expressed protein spots were analyzed using LTQ-FT-ICR MS. Of these proteins, 45 proteins were up-regulated in the treatment group, and 32 proteins were down-regulated. Analysis of LTQ-FI-ICR MS showed that about 50% of the proteins involved in carbohydrate metabolic process, metabolic process, and cellular metabolic compound salvage were affected by stress. Malate dehydrogenase protein and Glyceraldehyde-3-phosphate dehydrogenase protein related to carbohydrate metabolic process increased the level of protein expression in both 3 and 5-leaf stage under waterlogging stress. The increased abundance of these proteins may play an active role in response to waterlogging stress. These results provide new insights into the morphological alteration and modulation of differentially expressed proteins in sorghum cultivar.

• Mass Spectrometry Letters
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• 제3권4호
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• pp.93-100
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• 2012

Cellular processes such as proliferation, differentiation, and adaptation to environmental changes are regulated by protein phosphorylation. In order to enhance the understanding of molecular dynamics for biological process in detail, it is necessary to develop sensitive and comprehensive analytical methods for the determination of protein phosphorylation. Neural stem cells hold great promise for neural repair following an injury or disease. In this study, we made differentiated oligodendrocytes from human neural stem cells using over-expression of olig2 gene. We confirmed using quantitative phosphoproteome analysis approach that combines stable isotope labeling by amino acids in cell culture (SILAC) and $TiO_2$ micro-column for phosphopeptide enrichment with $MS^2$ and $MS^3$ mass spectrometry. We detected 275 phosphopeptides which were modulated at least 2-fold between human neural stem cells and oligodendrocytes. Among them, 23 phosphoproteins were up-regulated in oligodendrocytes and 79 phosphoproteins were up-regulated in F3 cells.

• Interdisciplinary Bio Central
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• 제1권3호
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• pp.9.1-9.6
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• 2009

Introduction: In the mass spectrometry-based proteomics, biological samples are analyzed to identify proteins by mass spectrometer and database search. Database search is the process to select the best matches to the experimental mass spectra among the amino acid sequence database and we identify the protein as the matched sequence. The match score is defined to find the matches from the database and declare the highest scored hit as the most probable protein. According to the score definition, search result varies. In this study, the difference among search results of different search engines or different databases was investigated, in order to suggest a better way to identify more proteins with higher reliability. Materials and Methods: The protein extract of human mesenchymal stem cell was separated by several bands by one-dimensional electrophorysis. One-dimensional gel was excised one by one, digested by trypsin and analyzed by a mass spectrometer, FT LTQ. The tandem mass (MS/MS) spectra of peptide ions were applied to the database search of X!Tandem, Mascot and Sequest search engines with IPI human database and SwissProt database. The search result was filtered by several threshold probability values of the Trans-Proteomic Pipeline (TPP) of the Institute for Systems Biology. The analysis of the output which was generated from TPP was performed. Results and Discussion: For each MS/MS spectrum, the peptide sequences which were identified from different conditions such as search engines, threshold probability, and sequence database were compared. The main difference of peptide identification at high threshold probability was caused by not the difference of sequence database but the difference of the score. As the threshold probability decreases, the missed peptides appeared. Conversely, in the extremely high threshold level, we missed many true assignments. Conclusion and Prospects: The different identification result of the search engines was mainly caused by the different scoring algorithms. Usually in proteomics high-scored peptides are selected and low-scored peptides are discarded. Many of them are true negatives. By integrating the search results from different parameter and different search engines, the protein identification process can be improved.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.121-121
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• 2017

The productivity of rice has been influenced by various abiotic factors including temperature which cause to limitations to rice yield and quality. Rice yield and quality are adversely affected by high temperature globally. In the present study, four Korean four cultivars such as Dongan, Ilpum, Samkwang, Chucheong were investigated in order to explore molecular mechanisms of high temperature at seedling stage. Rice seedlings grown at $28/20^{\circ}C$ (day/night) were subjected to 7-day exposure to $38/28^{\circ}C$ for high-temperature stress, followed by 2-D based proteomic analysis on biological triplicates of each treatment. The growth characteristics demonstrated that Dongan is tolerant while Ilpum is sensitive to high-temperature stress. High temperature has an adverse effect in the seedling stage both in high temperature sensitive and tolerant cultivar. Two-dimensional gels stained with silver staining, a total of 722 differential expressed protein spots (${\geq}1.5-fold$) were identified using Progenesis SameSpot software. However, a total of 38 differentially expressed protein spots were analyzed by LTQ-FT-ICR MS. Of these, 9 proteins were significantly increased while 10 decreased under high-temperature treatment. Significant changes were associated with the proteins involved in the carbohydrate metabolism, photosynthesis, and stress responses. Proteome results revealed that high-temperature stress had an inhibitory effect on carbon fixation, ATP production, and photosynthetic machinery pathway. The expression level of mRNA is significantly correlated with the results obtained in the proteome investigation. Taken together, these findings provide a better understanding of the high-temperature resistance by proteomic approaches, providing valuable insight into improving the high-temperature stress tolerance in the global warming epoch.

• 한국자원식물학회지
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• 제31권2호
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• pp.124-135
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• 2018

밭작물 중의 하나인 수수의 재배기간 중 장기간 지속되는 토양의 과습 상태는 수수의 생장 저하를 야기하는 요소로서 작용한다. 수수 잎을 이용한 수수의 3엽기, 5엽기 과습 처리시의 단백질을 동정한 결과 74개의 단백질들을 동정하였다. LTQ-FI-ICR MS로 분석한 결과 carbohydrate metabolic process, metabolic process, cellular metabolic compound salvage와 관련된 단백질들이 약50% 정도를 차지하며, 과습 스트레스를 받을 때 영향을 미치는 것으로 보였다. Carbohydrate metabolic process와 관련된 malate dehydrogenase 단백질과 glyceraldehyde-3-phosphate dehydrogenase 단백질은 과습 스트레스를 받았을 경우 3엽기와 5엽기 모두 단백질 발현양이 증가하였다. 이러한 단백질들은 과습 스트레스에 대한 antistress 기능을 하는 단백질로 알려져 있는데, 과습 스트레스에 반응하여 해당 단백질들의 발현양이 증가한 것으로 사료된다. 광합성과 관련된 oxygen-evolving enhancer protein 1 단백질은 대조구에서 보다 처리구에서 발현양이 다소 증가한 것을 볼 수 있었다. 또한, 3엽기에 비해서 5엽기에서 발현양이 증가한 것을 확인할 수 있었다. Response to oxidative stress와 관련된 probable phospholipid hydroperoxide glutathione peroxidase 단백질과 superoxide dismutase 단백질 모두5엽기 처리구에서 가장 많은 발현량을 보였다. 이는 과습 스트레스에 의한 활성산소 발생이 5엽기 처리구에서 가장 많았고, 이에 따라 항산화방어기작을 하는 단백질의 발현이 증가한 것으로 여겨졌다.