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Chen YL, Chang WH, Lee CY, Chen YR. An improved scoring method for the identification of endogenous peptides based on the Mascot MS/MS ion search. Analyst 2019; 144:3045-3055. [PMID: 30912770 DOI: 10.1039/c8an02141d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To identify endogenous peptides using MS/MS analysis and searching against a polypeptide sequence database, a non-enzyme specific (NES) search considering all of the possible proteolytic cleavages is required. However, the use of a NES search generates more false positive hits than an enzyme specific search, and therefore shows lower identification performance. In this study, the use of the sub-ranked matches for improving the identification performance of the Mascot NES search was investigated and a new scoring method was developed that considered the contribution of all sub-ranked random match probabilities, named the contribution score (CS). The CS showed the highest identification sensitivity using the Mascot NES search with a full protein database when compared to the use of the Mascot first ranked score and the delta score (DS). The confident peptides identified by DS and CS were shown to be complementary. When applied to plant endogenous peptide identification, the identification numbers of tomato endogenous peptides using DS and CS were 176.3% and 184.2%, respectively, higher than the use of the first ranked score of Mascot. The combination of DS and CS identified 200.0% and 8.6% more tomato endogenous peptides compared to the use of Mascot and DS, respectively. This method by combining the CS and DS can significantly improve the identification performance of endogenous peptides without complex computational steps and is also able to improve the identification performance of the enzyme specific search. In addition to the application in the plant peptidomics analysis, this method may be applied to the improvement of peptidomics studies in different species. A web interface for calculating the DS and CS based on Mascot search results was developed herein.
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Affiliation(s)
- Ying-Lan Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan 11529.
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Chen HJ, Shen YC, Shiao YJ, Liou KT, Hsu WH, Hsieh PH, Lee CY, Chen YR, Lin YL. Multiplex Brain Proteomic Analysis Revealed the Molecular Therapeutic Effects of Buyang Huanwu Decoction on Cerebral Ischemic Stroke Mice. PLoS One 2015; 10:e0140823. [PMID: 26492191 PMCID: PMC4619651 DOI: 10.1371/journal.pone.0140823] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 09/29/2015] [Indexed: 11/18/2022] Open
Abstract
Stroke is the second-leading cause of death worldwide, and tissue plasminogen activator (TPA) is the only drug used for a limited group of stroke patients in the acute phase. Buyang Huanwu Decoction (BHD), a traditional Chinese medicine prescription, has long been used for improving neurological functional recovery in stroke. In this study, we characterized the therapeutic effect of TPA and BHD in a cerebral ischemia/reperfusion (CIR) injury mouse model using multiplex proteomics approach. After the iTRAQ-based proteomics analysis, 1310 proteins were identified from the mouse brain with <1% false discovery rate. Among them, 877 quantitative proteins, 10.26% (90/877), 1.71% (15/877), and 2.62% (23/877) of the proteins was significantly changed in the CIR, BHD treatment, and TPA treatment, respectively. Functional categorization analysis showed that BHD treatment preserved the integrity of the blood–brain barrier (BBB) (Alb, Fga, and Trf), suppressed excitotoxicity (Grm5, Gnai, and Gdi), and enhanced energy metabolism (Bdh), thereby revealing its multiple effects on ischemic stroke mice. Moreover, the neurogenesis marker doublecortin was upregulated, and the activity of glycogen synthase kinase 3 (GSK-3) and Tau was inhibited, which represented the neuroprotective effects. However, TPA treatment deteriorated BBB breakdown. This study highlights the potential of BHD in clinical applications for ischemic stroke.
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Affiliation(s)
- Hong-Jhang Chen
- National Research Institute of Chinese Medicine, Taipei, Taiwan
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Yuh-Chiang Shen
- National Research Institute of Chinese Medicine, Taipei, Taiwan
| | - Young-Ji Shiao
- National Research Institute of Chinese Medicine, Taipei, Taiwan
| | - Kuo-Tong Liou
- Department of Chinese Martial Arts and Graduate Institute of Sport Coaching Science, Chinese Culture University, Taipei, Taiwan
| | - Wei-Hsiang Hsu
- National Research Institute of Chinese Medicine, Taipei, Taiwan
| | - Pei-Hsuan Hsieh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Ying Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail: (YLL); (YRC)
| | - Yun-Lian Lin
- National Research Institute of Chinese Medicine, Taipei, Taiwan
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, China Medical University, Taichung, Taiwan
- School of Pharmacy, National Taiwan University, Taipei, Taiwan
- * E-mail: (YLL); (YRC)
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Lin PC, Hu WC, Lee SC, Chen YL, Lee CY, Chen YR, Liu LYD, Chen PY, Lin SS, Chang YC. Application of an Integrated Omics Approach for Identifying Host Proteins That Interact With Odontoglossum ringspot virus Capsid Protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:711-26. [PMID: 25625820 DOI: 10.1094/mpmi-08-14-0246-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The glutamic acid at position 100 (E(100)) in the capsid protein (CP) of Odontoglossum ringspot virus (ORSV) plays an important role in long-distance viral movement in Nicotiana benthamiana. The ORSV(E100A) mutant, which has a glutamic acid to alanine substitution, shows a loss of systemic infectivity in N. benthamiana. Transmission electron microscopy and size-exclusion chromatography assays showed that E(100) is essential for CP-CP interaction and viral particle assembly. To identify the ORSV triggering or response genes and CP-interacting proteins (CP-IP), an integrated omics approach based on next-generation sequencing and proteomics profiling was used in this study. The whole-transcriptomes of healthy and ORSV-infected leaves of N. benthamiana were analyzed, and the gene information was used to create a N. benthamiana protein database that was used for protein identification following mass spectrometry analysis. The integrated omics approach identified several putative host proteins that interact with ORSV CP(WT) and were categorized as photosystem subunits, defense-associated proteins, and cell division components. The expression pattern and CP interaction of these CP-IP were examined by semiquantitative reverse transcription polymerase chain reaction and an in vitro binding assay, respectively, to verify the in silico data. Among these proteins, a proteinase inhibitor of N. benthamiana (NbPI2) was highly associated with CP(E100A) as compared with CP(WT), and NbPI1 and NbPI2 were highly induced in ORSV-infected plants. NbPI1- and NbPI2-silenced plants (via a Tobacco rattle virus-induced gene-silencing system) did not exhibit a difference in ORSV infection. Thus, whether NbPI1 and NbPI2 play a role in plant immunity requires further investigation. In summary, the integrated omics approach provides massive and valuable information to identify the ORSV CP-IP and these CP-IP will help us to understand the movement of this virus and plant-virus interaction.
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Affiliation(s)
- Pin-Chun Lin
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
- 2 Institute of Biotechnology, National Taiwan University, 81, Chang-Xing St., Taipei, Taiwan
| | - Wen-Chi Hu
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Shu-Chuan Lee
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Ying-Lan Chen
- 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan
- 5 Institute of Plant Biology and Department of Life Science, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Chi-Ying Lee
- 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan
| | - Yet-Ran Chen
- 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan
| | - Li-Yu Daisy Liu
- 6 Department of Agronomy, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Po-Yen Chen
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
| | - Shih-Shun Lin
- 2 Institute of Biotechnology, National Taiwan University, 81, Chang-Xing St., Taipei, Taiwan
- 3 Genome and Systems Biology Degree Program, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
- 4 Agricultural Biotechnology Research Center, Academia Sinica, 128, Academia Rd, Sec. 2, Taipei, Taiwan
| | - Ya-Chun Chang
- 1 Department of Plant Pathology and Microbiology, National Taiwan University, 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan
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Weng JH, Liang MR, Chen CH, Tong SK, Huang TC, Lee SP, Chen YR, Chen CT, Chung BC. Pregnenolone activates CLIP-170 to promote microtubule growth and cell migration. Nat Chem Biol 2013; 9:636-42. [PMID: 23955365 DOI: 10.1038/nchembio.1321] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/24/2013] [Indexed: 01/09/2023]
Abstract
Pregnenolone (P5) is a neurosteroid that improves memory and neurological recovery. It is also required for zebrafish embryonic development. However, its mode of action is unclear. Here we show that P5 promotes cell migration and microtubule polymerization by binding a microtubule plus end-tracking protein, cytoplasmic linker protein 1 (CLIP-170). We captured CLIP-170 from zebrafish embryonic extract using a P5 photoaffinity probe conjugated to diaminobenzophenone. P5 interacted with CLIP-170 at its coiled-coil domain and changed it into an extended conformation. This increased CLIP-170 interaction with microtubules, dynactin subunit p150(Glued) and LIS1; it also promoted CLIP-170-dependent microtubule polymerization. CLIP-170 was essential for P5 to promote microtubule abundance and zebrafish epiboly cell migration during embryogenesis, and overexpression of the P5-binding region of CLIP-170 delayed this migration. P5 also sustained migration directionality of cultured mammalian cells. Our results show that P5 activates CLIP-170 to promote microtubule polymerization and cell migration.
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Affiliation(s)
- Jui-Hsia Weng
- 1] Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan. [2] Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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Integration of Different "-omics" Technologies Identifies Inhibition of the IGF1R-Akt-mTOR Signaling Cascade Involved in the Cytotoxic Effect of Shikonin against Leukemia Cells. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013; 2013:818709. [PMID: 23861714 PMCID: PMC3703888 DOI: 10.1155/2013/818709] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/07/2013] [Indexed: 01/11/2023]
Abstract
Hematological malignancies frequently have a poor prognosis and often remain incurable. Drug resistance, severe side effects, and relapse are major problems of currently used drugs, and new candidate compounds are required for improvement of therapy success. The naphthoquinone shikonin derived from the Chinese medicinal herb, Lithospermum erythrorhizon, is a promising candidate for the next generation of chemotherapy. The basal cellular mechanism of shikonin is the direct targeting of mitochondria. Cytotoxicity screenings showed that the compound is particularly effective against leukemia cells suggesting an additional cellular mechanism. mRNA and miRNA microarrays were used to analyze changes in gene expression in leukemia cells after shikonin treatment and combined with stable-isotope dimethyl labeling for quantitative proteomics. The integration of bioinformatics and the three "-omics" assays showed that the PI3K-Akt-mTOR pathway was affected by shikonin. Deregulations of this pathway are frequently associated with cancerogenesis, especially in a wide range of hematological malignancies. The effect on the PI3K-Akt-mTOR axis was validated by demonstrating a decreased phosphorylation of Akt and a direct inhibition of the IGF1R kinase activity after shikonin treatment. Our results indicate that inhibiting the IGF1R-Akt-mTOR signaling cascade is a new cellular mechanism of shikonin strengthening its potential for the treatment of hematological malignancies.
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