胃幽門螺旋桿菌蛋白HP1442的結合區域與其受質之識別

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研究生：	楊淳竣 Chun-Jun Yang
論文名稱：	胃幽門螺旋桿菌蛋白HP1442的結合區域與其受質之識別 Identification of Binding Ligands and Association Region of HP1442 from Helicobacter pylori
指導教授：	程家維 Jya-Wei Cheng
口試委員:
學位類別：	碩士 Master
系所名稱：	生命科學暨醫學院 - 生物科技研究所 Biotechnology
論文出版年：	2006
畢業學年度：	94
語文別：	英文
論文頁數：	88
中文關鍵詞：	胃幽門螺旋桿菌、碳源調控蛋白、核磁共振
外文關鍵詞：	Helicobacter pylori, Carbon storage regulatory system, HP1442, NMR
相關次數：	點閱：4 下載：0
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胃幽門螺旋桿菌早在原始人離開非洲之前就已存在於胃中，並藉由人類的遷徙而散播到世界各地。目前，全世界仍有超過百分之五十的人口受到此菌種的感染，有時會造成消化性潰瘍或胃癌等嚴重疾病。雖然胃幽門螺旋桿菌已成功的發展出對抗極酸環境的特性，使其能夠在如此惡劣的環境之下，長期的生存在人類的胃壁黏膜上，但在其基因組內，卻只有少數能夠隨著環境改變而調節基因表現的調控因子。碳源儲存調控因子(CsrA)廣泛存在於許多不同的菌種中，為一核醣核酸鍵結蛋白，其調控機制屬於後轉錄層級，主要影響基因表現來適應環境大規模的改變。而在胃幽門螺旋桿菌中，亦可發現碳源儲存調控因子的蹤跡(HP1442)，但其調控的基因以及作用的目標序列尚不清楚。在此，我們利用SELEX (systematic evolution of ligands by exponential enrichment)的技術來辨識出HP1442的受質，其中大部分都包含AGGA的序列區段；並且收集一系列HP1442與受質混合後的 HSQC光譜，進而推測出HP1442與受質相互作用的區塊。

Helicobacter pylori was already present in the stomach of primitive humans as they left Africa and spread through the world. Today, it still chronically infects more than 50% of the human population, causing, in some cases, severe diseases such as peptic ulcers and stomach cancer. Although successful life-lasting habitation of such harsh environment is made by combination of several special characteristic of H. pylori to against the challenge of the extreme acidity, it possesses relatively few transcriptional regulators. The carbon storage regulator (CsrA) family of RNA-binding proteins are global post-transcriptional regulators that mediate extensive changes in gene expression in bacteria. Various homologs are found in broad range of different species, including H. pylori. However, the regulated genes and target sequences by CsrA homolog (HP1442) in H. pylori are still unclear. Ligands of HP1442 were identified from a combinational library using systematic evolution of ligands by exponential enrichment (SELEX). The SELEX derived sequences contained consensus AGGA elements. A series of 1H-15N heteronuclear single quantum coherence (HSQC) spectra with or without selected ligands were also acquired to find out the binding region of HP1442.

摘要    I
Abstract    II
List of Figure and Table    V
Chapter 1  Introduction    1
1.1. Structural Genomics    1
1.2. Helicobacter pylori    2
1.3. Carbon Storage Regulatory System    6
1.4. Summary    11
Chapter 2  Materials and Methods    21
2.1. Protein Sample Preparation    21
2.1.1 HP1442 and HP1442Δ16 Constructs    21
2.1.2 Protein Expression and Purification    21
2.2. Circular Dichroism Spectroscopy    23
2.3. SELEX    25
2.3.1 General Information    25
2.3.2 Experimental Procedure    26
2.4 Electrophoretic Mobility Shift Assay    28
2.5. NMR Spectroscopy    29
2.5.1 NMR Experiments Setup    29
2.5.2 Resonance Assignments    30
2.5.3 Dynamics Experiments    30
2.5.4 1H-15N HSQC Perturbation    31
Chapter 3  Results    37
3.1. Characterization of HP1442    37
3.1.1 Intrinsic Properties of HP1442 and HP1442Δ16    37
3.1.2 Conformational Analysis Based on Circular Dichroism (CD)    37
3.1.3 Amino Acid Sequence Alignment of HP1442    38
3.2. Hunting of HP1442 Ligands    39
3.2.1 SELEX Selection of HP1442 Ligands    39
3.2.2 Association of HP1442 and ssDNA    40
3.3. Resonance Assignment and Structure Calculation    40
3.3.1 Backbone Assignment    40
3.3.2 Side-chain Assignment    42
3.3.3 Secondary Structure Determination    42
3.3.4 Structure Calculation    44
3.4. 1H-15N HSQC Perturbation and Ligand Binding Site    46
Chapter 4  Discussion    75
4.1. SELEX Selection of HP1442 Ligands    75
4.2. Ligand Binding of CsrA    76
Reference    81


List of Figure and Table
Figure 1.1     Human migration and major Helicobacter pylori genotype distribution.    13
Figure 1.2     Schematic representation of infection process.    14
Figure 1.3     Helicobacter pylori.    15
Figure 1.4     Amino acid sequence alignments of CsrA homologs.    16
Figure 1.5     Predicted secondary structure of CsrB.    17
Figure 1.6     Model of CsrB interaction to inhibit CsrA.    18
Figure 1.7     Solution structure of CsrA from Escherichia coli.    19
Figure 1.8     Surface representation of CsrA.    20
Figure 2.1     Flowchart of SELEX procedure in ssDNA.    33
Figure 2.2     Acquisition parameters for NMR experiments of HP1442.    34
Table 2.1    Oligonucleotide Primers Used in PCR Amplifications    35
Figure 3.1     SDS-PAGE analysis of protein expression level in E.coli system.    49
Figure 3.2     Analytical ultracentrifuge experiments.    50
Figure 3.3     Conformation analysis based on CD spectroscopy.    51
Figure 3.4     Amino acid sequence alignment of HP1442.    52
Figure 3.5     SELEX selection of ssDNA ligands for HP1442 using random ssDNA pool.    53
Figure 3.6     Predicted secondary structures of the selected ssDNA ligands.    55
Figure 3.7     Gel mobility shift assay of HP1442 protein with ssDNA ligands.    56
Figure 3.8     Scalar connectivity obtained from HNCACB spectrum.    57
Figure 3.9     Scalar connectivity obtained from HNCA spectrum.    58
Figure 3.10     2D 1H-15N HSQC spectrum of HP1442 at 600 MHz.    59
Figure 3.11     2D 1H-15N HSQC spectrum of 15N labeled and selective labeled HP1442.    60
Figure 3.12     Consensus CSI plot.    61
Figure 3.13     2D 1H-15N HSQC of H/D exchange experiments.    62
Figure 3.14     Strip plots from 3D filtered NOESY experiments.    64
Figure 3.15     Rough structure of HP1442.    65
Figure 3.16     15N{1H} steady-state NOE experiments from HP1442.    66
Figure 3.17     CLEANEX-PM 15N-edited HSQC with mixing time 60 ms.    67
Figure 3.18     2D 1H-15N HSQC spectrum of HP1442D16 at 600 MHz.    68
Figure 3.19     Strip plots of 3D 15N-edited NOESY experiments from HP1442 and HP1442D16.    69
Figure 3.20     15N{1H} steady-state NOE experiments from HP1442D16.    70
Figure 3.21    (a) 1H-15N HSQC perturbation.    71
Figure 3.21    (b) Chemical shift changes versus residue number of HP1442    72
Figure 3.22      Surface properties of HP1442.    73
Figure 4.1    Comparison of CsrA and KH RNA-binding domain.    79
Figure 4.2    Analysis of glycogen overproduction.    80

                                

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