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研究生:陳靖怡
研究生(外文):Ching-Yi Chen
論文名稱:轉位子TnMERI1汞抗性操縱組轉錄調控因子之分子特性分析
論文名稱(外文):Molecular characterization of two MerR regulators and three operator/promoter regions in the mercury resistance module of TnMERI1
指導教授:黃介辰
學位類別:博士
校院名稱:國立中興大學
系所名稱:生命科學系所
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2008
畢業學年度:96
語文別:英文
論文頁數:45
中文關鍵詞:汞抗性操縱組調控MerR蛋白
外文關鍵詞:mer operonsregulationMerR protein
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Bacillus 轉位子 TnMERI1汞抗性決定因子的表現受到三個操作子/啟動子(O/PmerB3、O/PmerR1和O/PmerR2)以及兩個調控蛋白(MerR1和MerR2)所調控。為了釐清MerR1和MerR2蛋白的分子特性以及其在調控機制上扮演的角色,兩個調控蛋白分別被純化出來,並用以進行交聯實驗(cross-linking assay)及膠體阻滯實驗(gel shift assay)。結果顯示MerR1和MerR2蛋白都可以各自形成同質二聚體(homodimer)。由膠體阻滯實驗(gel shift assay)的結果得知,MerR1可以結合在O/PmerB3和O/PmerR1兩者的DNA調控區,而MerR2只專一性地結合於O/PmerR2的調控區。進一步利用限制內切酶保護實驗(restriction endonuclease protection assay)顯示MerR2結合O/PmerR2的位置落於啟動子–35和–10之間。此外也利用5’-RACE的方法,在原菌株(Bacillus megaterium strain MB1)中確定了O/PmerB3和O/PmerR2的轉錄起始點。在即時反轉錄聚合酶鏈鎖反應實驗(real-time reverse transcription PCR assay)中顯示,氯化汞(HgCl2)、醋酸苯汞(PMA)以及氯化甲基汞(MMC)都可以誘導啟動O/PmerB3和O/PmerR1表現,但是無法誘導啟動O/PmerR2表現。雖然,MerR2的誘導物仍待探討,本研究顯示MerR1可以調控O/PmerB3和O/PmerR1而MerR2只能調控O/PmerR2。
The expression of the mercury resistance module of Bacillus transposon TnMERI1 is regulated by three operator/promoter regions (O/PmerB3, O/PmerR1, and O/PmerR2) and two regulatory proteins (MerR1 and MerR2) encoded by the module itself. To elucidate the roles of MerR1 and MerR2 in the regulatory mechanism, both proteins were overexpressed and purified. In vitro cross-linking assays revealed that both MerR1 and MerR2 are capable of forming homodimers. MerR1 bound the regulatory regions O/PmerB3 and O/PmerR1, with a preference for O/PmerB3 as measured on in vitro gel shift assays and Kd analysis. However, MerR2 bound within the two hexamers of only O/PmerR2, as revealed by gel shift and restriction endonuclease protection assays (REPA). The transcriptional start sites of O/PmerB3 and O/PmerR2 were determined by rapid amplification of 5’-cDNA ends (5’-RACE) in the TnMERI1 original host, Minamata Bay isolated Bacillus megaterium strain MB1. The results of real-time reverse transcription PCR assay showed that O/PmerB3 and O/PmerR1 were induced in the presence of mercuric inducers but not O/PmerR2. Though the inducer for MerR2 remained to be determined, it can be suggested that MerR1 regulates O/PmerB3 and O/PmerR1, while MerR2 regulates O/PmerR2.
ACKNOWLEDGMENTS i
ABSTRACT IN CHINESE ii
ABSTRACT IN ENGLISH iii
CONTENTS iv
LIST OF FIGURES vii
CHAPTER 1 INTRODUCTION 1
1.1 What are heavy metals? 1
1.2 Microbial heavy metal resistance mechanisms 2
1.3 Bacterial mercury resistance system 4
1.4 The structure of mer operons 6
1.5 Regulation of mer gene expression 7
1.5.1 The MerR protein 8
1.5.2 The mer operator/promoter 9
1.5.3 The MerD protein 10
1.6 The mercury resistance module of Bacillus transposon TnMERI1 10
1.7 Purpose of study 12
CHAPTER 2 MATERIALS AND METHODS 14
2.1 Bacterial strains, plasmids, media, and growth conditions 14
2.2 Cloning, transformation, and DNA manipulation 14
2.3 Preparation of RNA 15
2.4 Rapid amplification of 5’-cDNA ends (5’-RACE) 15
2.5 Construction of expression plasmids for purification of MerR proteins 16
2.6 Purification of MerR1 protein 17
2.7 Purification of MerR2 protein 19
2.8 Protein quantification 19
2.9 Glutaraldehyde cross-linking assays of MerR1 or MerR2 protein 20
2.10 Amplification of mer operator/promoter regions by PCR 20
2.11 Gel shift assay 21
2.12 Restriction endonuclease protection assay (REPA) 22
2.13 Real-time reverse transcriptase PCR 23
CHAPTER 3 RESULTS 25
3.1 Identification of the transcriptional start sites by rapid amplification of 5’-cDNA ends (5’-RACE) 25
3.2 Purification of MerR1 and MerR2 25
3.3 Glutaraldehyde cross-linking assays of MerR1 and MerR2 26
3.4 Interactions of the two regulatory proteins and the three mer operators 26
3.5 Apparent dissociation constants (Kd) of the regulatory protein-operator complexes 27
3.6 Restriction endonuclease protection assay (REPA) for O/PmerR2 28
3.7 Real-time RT-PCR measurements of expression from the three mer promoters with different inducers in B. megaterium strain MB1 30
CHAPTER 4 DISCUSSION 31
CHAPTER 5 CONCLUSION 35
REFERENCES 36
TABLE AND FIGURES 46

LIST OF FIGURES
Figure 1. Organization of mer operons and Mer proteins 47
Figure 2. Multiple sequences alignment of MerR1, MerR2, MerR, and MerD proteins from a variety of Gram-positive and -negative mer operon by using Clustal W (1.81) 48
Figure 3. The genetic structure of mercury resistance module of the class II transposon TnMERI1 found from Gram-positive bacteria B. megaterium strain MB1 49
Figure 4. Nucleotide sequences of the three mer operator/promoter regions from mercury resistance module of transposon TnMERI1 50
Figure 5. Construction of MerR1 and MerR2 expression vectors 51
Figure 6. Confirmation of the pET-MerR1 and pET-MerR2 by restriction enzyme digestion 52
Figure 7. Over-expression and purification of MerR1 and MerR2 proteins 53
Figure 8. Edman degradation (six cycles) was performed to determine N-terminal amino acid sequence of the purified MerR1 protein 54
Figure 9. Edman degradation (six cycles) was performed to determine N-terminal amino acid sequence of the purified MerR2 protein 55
Figure 10. Glutaraldehyde cross-linking assay of MerR1 or MerR2 56
Figure 11. Gel shift assays of the O/PmerB3, O/PmerR1, and O/PmerR2 DNA fragments with (A) MerR1 and (B) MerR2 proteins 57
Figure 12. Quantitative analysis for (A) MerR1-O/PmerB3, (B) MerR1-O/PmerR1, and (C) MerR2-O/PmerR2 with (right) or without (left) 1 μM HgCl2 58
Figure 13. Restriction endonuclease protection assay (REPA) for the (B) AclI and (C) DdeI restriction sites in the merR2 operator/promoter region of (A) plasmid pGEM-O/PmerR2 59
Figure 14. Relative amounts of merB3, merR1, and merR2 mRNA measured in B. megaterium strain MB1 by real-time RT-PCR 60
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