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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 吳世雄(Shih-Hsiung Wu) | |
dc.contributor.author | Wan-Ling Wu | en |
dc.contributor.author | 吳婉鈴 | zh_TW |
dc.date.accessioned | 2021-06-16T08:30:09Z | - |
dc.date.available | 2014-01-27 | |
dc.date.copyright | 2014-01-27 | |
dc.date.issued | 2013 | |
dc.date.submitted | 2013-12-30 | |
dc.identifier.citation | References
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dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/58771 | - |
dc.description.abstract | 蛋白質的磷酸化作用在細菌體內已被視為一種很重要的蛋白質轉錄後修飾,因此研究細菌的磷酸蛋白質體學便可提供一項相當有用的資訊,用以了解細菌生理過程中的整個調控網絡。因此,在本篇研究中,利用散彈式方法去分析極端嗜熱菌株HB27的磷酸蛋白質體學,此嗜熱菌屬是從自然界的高熱溫泉水中被分離出來的,因其帶有高頻率的自然勝任作用,因此這個菌屬已被當作是嗜熱菌中的模式生物,用以研究第四型纖毛的分子機制如何導致高頻率勝任作用,因為其附帶在胞外的纖毛附屬物具多功能性,例如可以從高熱環境中攝取外來核酸物質的能力即是勝任作用,除此之外,還包括具有能貼附到不同介質以及在高溫環境中形成生物膜的能力。因此根據本篇的實驗結果顯示總共有93條個別的磷酸化胜肽片段和67個磷酸化位置可以被檢測到,這些被鑑定到的磷酸胜肽分別來自胞內的53個磷酸化蛋白質。再近一步依據其磷酸化位置分布在絲氨酸(Ser)、蘇氨酸(Thr)、和酪胺酸(Tyr)上的比例可以被計算為57% /63% /7%;當依其功能做分類時,這些磷酸化蛋白質大部分參與在中央代謝路徑和合成蛋白質或細胞壁膜的功能。再依其胺基酸序列和其他菌種的磷酸化蛋白質相互比對來分析同源蛋白質之間的演化保留度時,結果顯示大部分被檢測到參與在中央代謝路徑的這些磷酸化蛋白質的磷酸化位置和兩側胺基酸序列皆呈現高度保留性。有趣的是,不論是我們找到的四個被磷酸化的耐熱磷酸醣轉移酶和與此蛋白質同源的磷酸化位置皆可鑑定到一個被高度保留的絲氨酸磷酸化修飾。另外,我們也發現這些可以參與在蛋白質合成裝置中以及細胞壁膜生合成的磷酸化蛋白質與調控此菌的高溫適應能力有所關聯。為了更進一步證實這項假設,藉由找到的PilF磷酸化蛋白質,第一次在我們的分析結果中發現在蘇氨酸第368號位置以及絲氨酸第372號位置可以被磷酸化。PilF已知是一個參與在第四型纖毛合成相關的蛋白質,其具有可分解ATP的活性,透過點突變的方式將蘇氨酸第368號位置突變成天門冬氨酸(Asp)和絲氨酸第372號位置突變成榖氨酸(Glu)用以模擬磷酸化作用時,結果發現可以導致第四型纖毛的消失以及失去抽扯性運動;相反的,當蘇氨酸第368號位置突變成擷氨酸(Val)和絲氨酸第372號位置突變成丙氨酸(Ala)用以模擬去磷酸化作用時,又可引發纖毛組成和恢復抽扯性運動的功能。另外也發現當HB27菌株大量表現這些被置換成模擬磷酸化作用的點突變PilF時,可藉由快速地貼附在固態介質上並且伴隨產生相對量多的胞外多醣,幫助提升生物膜生成的能力。因此,由以上結果得知PilF的蛋白質磷酸化修飾可以調控纖毛組成和生物膜形成伴隨著胞外多醣的分泌。總結來說,本篇針對極端嗜熱性細菌的磷酸化蛋白質體學研究,可以清楚地指出被磷酸化的這些耐熱性磷酸化蛋白質,可能扮演著在高溫環境中去調控許多代謝路徑及適應高溫過程中的重要角色。 | zh_TW |
dc.description.abstract | Protein phosphorylation has been established as an important post-translational modification in bacterial cells. Bacterial phosphoproteomics provides a better understanding of the regulatory networks in physiological processes. In this study, the shotgun approach was applied to analyze the phosphoproteome of the extremely thermophilic eubacterium T. thermophilus HB27. The genus Thermus isolated from its natural hot spring environment with a high frequency of natural competence often used as a thermophilic model to investigate the molecular basis of type IV pili (T4P)-mediated functions, such as the uptake of free DNA, adhesion, twitching motility, and biofilm formation, in hot environments. Ninety-three unique phosphopeptides, including 67 in vivo phosphorylated sites on 53 phosphoproteins, were identified. The distribution of Ser/Thr/Tyr phosphorylation sites was 57%/36%/7%. The phosphoproteins were mostly involved in central metabolic pathways and protein/cell envelope biosynthesis. Sequence alignment and comparison revealed that the identified phosphoproteins, phosphosites, and their flanked regions involved in central metabolic pathways were highly conserved. Interestingly, four phosphosugar mutases were phosphorylated on a conserved serine residue and also found in all studied prokaryotic phosphoproteomes. According to this analysis, the identified phosphoproteins such as chaperonin GroEL, DAG kinase, MurE, and PilF involved in the protein synthesis machinery and regulation of cell envelope biosynthesis were correlated with thermoadaptation. Moreover, the ATPase motor PilF, a T4P-related component, was first found to be phosphorylated on Thr-368 and Ser-372. Through the point mutation of PilF, mimic phosphorylated mutants T368D and S372E resulted in the nonpiliated and nontwitching phenotypes, whereas non-phosphorylated mutants T368V and S372A displayed piliation and twitching motility. In addition, mimic phosphorylated mutants showed elevated biofilm-forming abilities with higher initial attachment rate, caused by increasing exopolysaccharide production. Therefore, the phosphorylation of PilF might regulate the pili and biofilm formation associated with exopolysaccharide production. In summary, this study of thermophilic bacteria phosphoproteomics indicated that phosphorylated thermostable proteins may play important roles in regulating many metabolic pathways and adaptation processes in a thermal environment. | en |
dc.description.provenance | Made available in DSpace on 2021-06-16T08:30:09Z (GMT). No. of bitstreams: 1 ntu-102-D96b46006-1.pdf: 14711488 bytes, checksum: f6c5f021082a9b7af4e0b75e28db3b81 (MD5) Previous issue date: 2013 | en |
dc.description.tableofcontents | 目錄
誌謝 i 中文摘要 ii 英文摘要 iv 目錄 vi Abbreviations x List of Figures xii List of Tables xiv Chapter 1 Phosphoproteomic Analysis of Thermophilic Bacterium Thermus thermophilus HB27 1.1 Introduction 1 1.1.1 Protein phosphorylation in bacteria 1 1.1.2 Mass spectrometry (MS)-based phosphoproteomics 2 1.1.3 Phosphoproteome enrichment strategies 5 1.1.4 The feature of extremely thermophilic T. thermophilus HB27 7 1.1.5 Aims and experimental approaches 9 1.2 Materials and Methods 11 1.2.1 Growth conditions and protein extraction 11 1.2.2 Protein digestion and phosphopeptide enrichment 11 1.2.3 Liquid chromatography–mass spectrometric analysis 12 1.2.4 Data processing and validation 12 1.2.5 Bioinformatics analysis 14 1.2.6 Phosphoprotein 3D structure modeling 14 1.3 Results 15 1.3.1 Phosphoproteome of exponentially growing T. thermophilus HB27 15 1.3.2 Classification of the identified phosphoproteins 19 1.3.3 Phosphoproteins involved in central metabolic pathways 19 1.3.4 Phosphoproteins involved in nucleotide metabolic pathways 28 1.3.5 Phosphoproteins involved in protein biosynthesis 33 1.3.6 Phosphoproteins involved in cell envelope biosynthesis 34 1.4 Discussion 37 1.4.1 Comparison of total phosphoproteins conserved in T. thermophilus HB27 and other bacteria 37 1.4.2 The importance of the phosphosites identified and conserved in T. thermophilus HB27 and other bacteria 40 1.4.3 Importance of the phosphoproteins in nucleotide metabolism 41 1.4.4 The importance of the phosphoproteins essential to protein biosynthesis 44 1.4.5 Importance of phosphoproteins to cell envelope biosynthesis 45 1.4.6 Prospective on the bacterial phosphoproteome analysis 48 1.5 Conclusion 50 Chapter 2 Functional analysis of PilF phosphorylation reveals the effects on Type IV pilus and biofilm formation in Thermus thermophilus HB27 2.1 Introduction 51 2.1.1 Overview the biological significance of the Ser/Thr/Tyr protein phosphorylation in bacteria 51 2.1.2 Protein secretion systems in bacteria and phosphorylation regulation 54 2.1.3 Type IV pilus (T4P)-mediated functions in T. thermophilus HB27 55 2.1.4 The unique roles of PilF in T. thermophilus HB27 57 2.1.5 Biofilm formation and exopolysaccharide (EPS) production in T. thermophilus HB27 60 2.1.6 Aim and experimental approaches 61 2.2 Materials and Methods 63 2.2.1 Bacterial strains and growth conditions 63 2.2.2 Construction of PilF expression plasmids and site-directed mutagenesis 63 2.2.3 Overexpression of recombinant PilFs in T. thermophilus HB27 65 2.2.4 Expression and purification of recombinant PilFs in E. coli 66 2.2.5 Phosphorylation stoichiometry estimation 67 2.2.6 LC-MS/MS analysis 67 2.2.7 ATPase activity assay 68 2.2.8 Circular dichroism (CD) spectra 68 2.2.9 Analytical ultracentrifugation (AUC) analysis 69 2.2.10 Scanning electron microscopy (SEM) of biofilm architecture 69 2.2.11 Transmission electron microscopy (TEM) of T4P 69 2.2.12 Biofilm formation assays 70 2.2.13 Quantitative measurement of exopolysaccharides (EPS) 70 2.2.14 Sugar composition 71 2.3 Results 72 2.3.1 Phosphorylation of Thr368 and Ser372 residues of the ATP-binding motif-containing protein PilF 72 2.3.2 Effects of site-directed mutagenesis of PilFs on colony morphology and piliation 72 2.3.3 Effects of site-directed mutagenesis of PilFs on biofilm formation and EPS production 78 2.4 Discussion 88 2.4.1 Protein phosphorylation regulates T4P-mediated functions in T. thermophilus HB27 88 2.4.2 Phosphorylated PilF interferes with pilus formation and retards motility in T. thermophilus HB27 88 2.4.3 Phosphorylated PilF increases EPS production and thus enhances biofilm formation 89 2.5 Conclusion 92 Acknowledgments 93 References 94 Appendix 104 Appendix 1-1. The detailed list of the identified phosphoproteins in T. thermophilus HB27 104 Appendix 1-2. The detailed list of the identified phosphoproteins in T. thermophilus HB27 106 Appendix 2. Information of KEGG pathway, motifs, and evolutionary analysis of phosphoproteins in T. thermophilus HB27. 108 Appendix 3. MS/MS spectra 111 | |
dc.language.iso | en | |
dc.title | 磷酸化蛋白質體學分析顯示嗜熱菌株HB27之磷酸化蛋白PilF影響第四型纖毛及生物膜生成 | zh_TW |
dc.title | Phosphoproteomic analysis reveals the effects of PilF phosphorylation on type IV pilus and biofilm formation in Thermus thermophilus HB27 | en |
dc.type | Thesis | |
dc.date.schoolyear | 102-1 | |
dc.description.degree | 博士 | |
dc.contributor.oralexamcommittee | 邱繼輝(Kay-Hooi Khoo),蔡明道(Ming-Daw Tsai),張文章(Wen-Chang Chang),陳水田(Shui-Tein Chen),梁博煌(Po-Huang Liang) | |
dc.subject.keyword | 嗜熱性菌屬,磷酸化蛋白質體學,陰離子交換樹酯和二氧化鈦親和性磷酸胜?萃取,質譜儀分析儀/第四型纖毛/ATP分解?活性PilF蛋白質/抽扯性運動/生物膜生成/胞外多糖產生, | zh_TW |
dc.subject.keyword | Thermus thermophilus,phosphoproteome,SCX-TiO2 phosphopeptide enrichment,Mass spectrometry,type IV pili,ATPase PilF,twitching motility,biofilm formation,exopolysaccharide production, | en |
dc.relation.page | 134 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2013-12-31 | |
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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