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http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/79467完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 林俊宏(Chun-Hung Lin) | |
| dc.contributor.author | Bolor Buyanbadrakh | en |
| dc.contributor.author | 柏樂 | zh_TW |
| dc.date.accessioned | 2022-11-23T09:01:15Z | - |
| dc.date.available | 2021-11-05 | |
| dc.date.available | 2022-11-23T09:01:15Z | - |
| dc.date.copyright | 2021-11-05 | |
| dc.date.issued | 2021 | |
| dc.date.submitted | 2021-10-22 | |
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/79467 | - |
| dc.description.abstract | "肽聚醣 (peptidoglycan, PG) 細胞壁是所有細菌中必不可少的重要組成部分，其合成是通過動態或是瞬時的多蛋白複合物進行的。革蘭氏陰性菌之大腸桿菌(Escherichia coli)具有獨特的 PG 合成複合物，包括延長體、分裂體和兩種 A 類的青黴素結合蛋白（penicillin binding proteins, PBPs）。這些生化實體催化基本相同的反應，近期的研究已經確定它們的特殊功能，主要是基於波動的環境條件下，對其突變表型的分析。儘管 PG 合成複合物重要的動態特性已被廣泛接受，但尚未有系統地研究複合物與主成分之間的相互作用。在這裡，我們開發了一種強親和力的富集質譜實驗平台，將複合物保留在其天然的膜結合環境中，且 PG 合成複合物 PBP1a、PBP1b、PBP2、MreB和 FtsZ 分別與弱/瞬態夥伴進行結合。為了將複合物保留在其天然條件下，我們設計大腸桿菌菌株，透過內源性表達之誘餌蛋白和親和標籤相融合。將化學交聯劑應用於活細菌樣品和蛋白質之間的交聯作用，並使用苯乙烯馬來酸 (SMA) 在膜結合的天然環境中提取蛋白質複合物。純化的複合物用於質譜分析以進行蛋白質鑑定。我們在上述五種誘餌蛋白的相互作用組中鑑定了 971 個獨特的結合夥伴。豐富的功能性分析允許識別其不同功能間的關聯性。用定量數據集探索其誘餌蛋白的相對特異性，並確定其潛在的誘餌特異性蛋白之相互作用物。此處介紹的主要 PG 合成和調節蛋白間的相互作用組，並針對功能冗餘蛋白提供獨特的見解，作為其保守且實質重要的細菌系統中不同的相互作用組模塊的藍圖。 " | zh_TW |
| dc.description.provenance | Made available in DSpace on 2022-11-23T09:01:15Z (GMT). No. of bitstreams: 1 U0001-1210202106160200.pdf: 14716330 bytes, checksum: eea1d4218687b65fe5cb490fe250462b (MD5) Previous issue date: 2021 | en |
| dc.description.tableofcontents | "Acknowledgement i 摘要 iv Abstract v Table of Contents vii List of Figures x List of Tables xii Abbreviations xiii 1. Introduction 1 1.1. Bacterial cell wall and its importance to drug development 1 1.2. Bacterial cell wall synthesis and cell wall synthesizing complexes 2 1.3. Importance of functional redundancy in bacterial cell wall synthesis 7 1.4. Applications of affinity enrichment mass spectrometry-based proteomics for interactome studies 10 2. Thesis rationale and aim 13 3. Materials and Methods 14 3.1. Bacterial strain construction 14 3.1.1. Strain construction overview 15 3.1.2. Bacterial strains, plasmids and standard growth conditions 16 3.1.3. Polymerase chain reaction (PCR) 17 3.1.4. Agarose gel electrophoresis and DNA extraction from agarose gel 22 3.1.5. Preparation of electro-competent cell and storage 23 3.1.6. Electroporation and cell recovery 23 3.1.7. Antibiotic resistant cassette removal 23 3.1.8. DNA sequencing 24 3.1.9. Automated growth analysis 24 3.1.10. Microscopic observation of bacterial cell morphology 224 3.2. In vivo protein cross-linking 25 3.2.1. Counting of surface lysine of protein 25 3.2.2. Protein cross-linking 25 3.3. E. coli membrane protein solubilization 26 3.3.1. Preparation of styrene maleic acid (SMA) co-polymer from styrene maleic anhydride co-polymer 26 3.3.2. Total membrane isolation 26 3.3.3. Solubilization of membrane protein using Styrene Maleic Acid (SMA) 27 3.3.4. Transmission electron microscopy negative staining analysis of SMALP 27 3.4. Analysis of protein sample 28 3.4.1. Estimation of protein quantity of SMALP samples 28 3.4.2. Western blotting analysis 28 3.5. Affinity enrichment mass spectrometry analysis 29 3.5.1. Experimental design 29 3.5.2. Poly-histidine tagged protein complex enrichment 30 3.5.3. Mass spectrometry (MS) front-end sample preparation 31 3.5.4. Mass spectrometry data acquisition 32 3.5.5. MS raw data processing and quality check 32 3.6. Bioinformatic analysis 33 3.6.1. Data pre-processing on Perseus software platform 33 3.6.2. Data quality check and statistical analysis 34 3.6.3. Functional enrichment analysis 35 3.6.4. Subcellular topology annotation of proteins 35 3.6.5. Protein-protein interaction network construction 36 3.6.6. Statistical analysis to identify bait specific binding partners 36 4. Results 37 4.1. Experimental platform to enrich protein complexes in near native membrane bound environment 37 4.1.1. Results of non-invasive bacterial gene engineering 37 4.1.2. In vivo protein cross-linking: assessment of cross-linker accessibility 40 4.1.3. Obtaining hydrolyzed SMA and membrane protein solubilization in SMALP 43 4.1.4. Mass spectrometry proteomics data analysis 46 4.1.5. Identifying of protein binding partners of bait proteins by statistical analysis 49 4.1.6. Functional annotation and enrichment analysis 53 4.1.7. The identification of the functional differentiation based on the differential enrichment profile 58 4.1.8. Validation of interactome with protein-protein interaction database 62 4.2. Exploring protein specificity with quantitative AE - MS 68 5. Discussion 78 5.1. Affinity enrichment mass spectrometry experimental platform 78 5.2. Exploring associated biological functions in interactome 80 5.3. Statistical methods 83 6. Conclusions and Future Directions 85 6.1. Summary 85 6.2. Future directions 86 References 87 Supplementary 97 " | |
| dc.language.iso | en | |
| dc.title | 透過親和力富集質譜平台比較大腸桿菌中肽聚醣合成複合物的相互作用組分析 | zh_TW |
| dc.title | Comparative interactome analysis of the peptidoglycan synthesizing complexes in Escherichia coli | en |
| dc.date.schoolyear | 109-2 | |
| dc.description.degree | 博士 | |
| dc.contributor.coadvisor | 梁素雲(Suh-Yuen Liang),馬徹(Che Ma) | |
| dc.contributor.oralexamcommittee | 呂桐睿(Hsin-Tsai Liu),安形高志(Chih-Yang Tseng),邱繼輝 | |
| dc.subject.keyword | 肽聚醣合成,相互作用組,親和力富集質譜, | zh_TW |
| dc.subject.keyword | Peptidoglycan synthesis,interactome,affinity enrichment mass spectrometry, | en |
| dc.relation.page | 122 | |
| dc.identifier.doi | 10.6342/NTU202103656 | |
| dc.rights.note | 同意授權(全球公開) | |
| dc.date.accepted | 2021-10-22 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 生化科學研究所 | zh_TW |
| 顯示於系所單位： | 生化科學研究所 | |
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