List of abbreviations and measurement units

Table of contents
List of abbreviations and measurement units

i

Table of contents

iii

List of Figures

xii

List of Tables

xv

List of Publications

xvi


Abstract

xvii

Declaration

xix

Acknowledgements

xx

Chapter 1. General Introduction

1

Chapter 2. Literature Review

3


2.1 The mammalian mitochondrial genome

3

2.1.1 Gene expression

4

2.1.1.1 Gene transcription

5

2.1.1.2 RNA processing

8

2.1.1.3 Translation

9


2.1.2 Replication and maintenance of mtDNA
2.2 Human mitochondrial diseases

12
17

2.2.1 Mitochondrial defects related to mtDNA mutation/rearrangements

17

2.2.2 Disease manifestations: threshold level and complementation

18

2.3 Animal models of mitochondrial disease

20

2.3.1 Mitochondrial transgenic mice


20

2.3.2 Methods for the generation of transmitochondrial transgenic mice

23

2.3.3 Model systems for transmitochondrial mice

25

2.4 Gene targeting of mitochondria

27

2.4.1 Mitochondrial DNA constructs

27

2.4.2 Mitochondrial internalization of nucleic acids


29

2.4.2.1 Mitochondrial compartments

30

2.4.2.2 Import of rRNA and tRNA

31

2.4.2.3 How can nucleic acids be targeted to mitochondria?

32

2.4.2.3.1 Cis-acting elements

32

iii


2.4.2.3.2 Cytoplasmic factors

34

2.4.2.3.3 Conformation changes

35

2.4.2.3.4 Mitochondrial protein complexes facilitate import?

35

2.5 Mitochondrial DNA delivery systems

37

2.5.1 Targeting molecules into mitochondria

38


2.5.2 Liposome mediated import of exogenous DNA

40

2.5.3 DQAsome

42

2.5.3.1 Micellar form of dequalinium

42

2.5.3.2 Cytotoxicity of dequalinium

43

2.5.3.3 Dequalinium induces a selective loss of mtDNA.

43


2.5.3.4 Dequalinium unwinds DNA

44

2.5.3.5 Effect of dequalinium on cytochrome c oxidase activity

45

2.5.3.6 Effect of culture medium on dequalinium cytotoxicity

45

2.6 Scope of thesis

Chapter 3. General Materials and Methods

46
47
47


3.1 DNA
3.1.1 DNA purification

47

3.1.1.1 Extractionof DNA fragments from agarose gels

47

3.1.1.2 Purification of PCR products

48

3.1.1.3 Minipreps

48

3.1.1.4 Maxipreps

49


3.1.2 Ligation

51

3.1.3 E. coli transformation and plasmid propagation

51

3.1.4 Glycerol stock

52

3.1.5 DNA sequencing

52

3.2 Cell culture

53


3.2.1 Cell lines

53

3.2.2 Culture conditions

53

3.2.3 Cell harvesting

54

3.2.4 Freezing and thawing of cell stocks

55

3.2.5 Assays for cell viability

55

3.3 Transfection

56

iv

3.3.1 Transfection reagent

56

3.3.1.1 DQAsome preparation

56

3.3.1.2 Plasmid vectors

57

3.3.1.3 Preparation of lipoplex (liposome-DNA)

57

3.3.2 Transfection assays

58

3.3.2.1 Lipofectin protocols for transient transfection

58

3.3.2.1 DQAsome protocols for transfection

58

3.4 Mitochondria isolation

59

3.5 PCR protocols

60

3.5.1 General PCR

60

3.5.2 PCR for cellular pmtGFP DNA detection.

61

3.5.3 RT-PCR for mtgfp transcripts

62

3.6 Site directed mutagenesis

63

3.6.1 Basic principle of site directed mutagenesis

63

3.6.2 Mutagenesis primer design

64

3.6.3 Mutant strand synthesis

64

3.6.4 Ligation of PCR product

65

3.6.5 Dpn I digestion of the plasmid template

65

3.6.6 Transformation of ultracompetent cells

65

3.7 Flow cytometry

66

3.8 Microscopy

66

3.8.1 Epifluorescence microscopy

66

3.8.2 Confocal microscopy

66

3.9 Freeze-thaw-cultured of transfected cells

67

3.10 Fluorescence in Situ Hybridization (FISH)

67

3.10.1 Preparation of the hybridization probe

67

3.10.2 Nick translation

68

3.10.3 Purification of amine-modified DNA

68

3.10.4 Labeling with a reactive fluorescent dye

69

3.10.5 In situ hybridization

70

3.10.6 Hoechst 33342 staining

71

3.11 Animals
3.11.1 Mice

71
71

v

3.11.2 Strains

71

3.11.3 Husbandry (female and male)

71

3.11.4 Embryo

72

3.11.4.1 Superovulation

72

3.11.4.2 Mating

72

3.11.4.3 Embryo collection and cumulus cells removal

72

3.11.4.4 Zona pellucida removal

73

3.11.4.5 In vitro embryo culture

73

Chapter 4. Construction of an artificial mitochondrial genome
expressing GFP
4.1 Introduction

74
74

4.1.1 Small genome to facilitate mitochondrial internalization and maintenance 75

4.1.2 Green fluorescent protein (gfp) as a mitochondrial reporter gene

76

4.1.3 Mitochondrial complementation

78

4.2 Materials and Methods

79

4.2.1 Oligonucleotides

79

4.2.2 Generation of a mitochondrial gfp gene (mtgfp)

79

4.2.3 Assembly of pmtGFP

80

4.2.4 E. coli transformation and plasmid propagation

81

4.2.5 pmtGFP and pmtBFP sequencing

82

4.2.6 pmtGFP mutagenesis to generate pmtBFP

82

4.2.7 Cell culture

82

4.2.8 Plasmid vector

82

4.2.9 Transfection reagent and preparation of lipoplex

83

4.2.10 Transfection assay

83

4.2.11 Fluorescence in situ hybridization (FISH)

83

4.2.12 Epifluorescence microscopy

84

4.3 Results

84

4.3.1 Generation of the minimitochondrial genome construct pmtGFP

84

4.3.2 Blue fluorescence variant of pmtGFP

91

4.3.3 Expression of pmtGFP following its introduction into cell nuclei

91

4.4 Discussion

95

vi

4.4.1 Construction of an artificial mouse mitochondrial genome expressing
GFP

95

4.4.2 The mitochondrial GFP construct

96

4.4.3 The blue fluorescence variant of pmtGFP

98

4.4.4 The minimitochondrial construct pmtGFP is not expressed in the
cytosol

98

4.5 Conclusions

Chapter 5. DQAsome as a mitochondrial DNA delivery system

100

101

5.1 Introduction

101

5.2 Materials and Methods

102

5.2.1 Cell culture

102

5.2.2 Transfection reagents

103

5.2.3 Plasmid vectors

103

5.2.4 Preparation of lipoplex

103

5.2.5 Transfection assays

103

5.2.6 DQAsome cytotoxicity assessments

104

5.2.6.1 Cell growth

104

5.2.6.2 Trypan blue staining

104

5.2.6.3 Mitochondrial JC-1 staining

104

5.2.7 Mitochondrial internalization of pmtGFP DNA

105

5.2.7.1 Fluorescence in situ hybridization (FISH)

105

5.2.7.2 PCR for mtgfp detection

106

5.2.8 Confirmation of mitochondrial GFP expression

106

5.2.8.1 RT-PCR for mtGFP transcription

106

5.2.8.2 Epifluorescence microscopy

106

5.2.8.3 Flow cytometry (FACS Analysis)

107

5.2.8.4 Confocal microscopy

107

5.2.9 Exogenous mtDNA preservation

107

5.2.10 Freezing, thawing and culturing transfected cells

107

5.3 Results

108

5.3.1 DQAsome is cytotoxic at high concentrations

108

5.3.2 Mitochondrial internalization of pmtGFP

113

vii

5.3.2.1 Distribution of transfected DNA within cells

113

5.3.2.2 Localization of plasmid DNA in cells transfected with
DQAsome-pmtGFP lipoplex

114

5.3.2.3 Detection of pmtgfp DNA in the mitochondrial fraction of
transfected cells

114

5.3.3 Analysis of mitochondrial GFP expression

116

5.3.3.1 mtgfp transcription using RT-PCR assays

116

5.3.3.2 Time lapse pmtGFP expression post-transfection

116

5.3.3.3 Efficiency of transfection: FACS analysis

120

5.3.3.4 Colocalization of the pmtGFP DNA signal and GFP
expression in transfected cells

121

5.3.4 Mitochondrial preservation of exogenous DNA

122

5.3.5 Persistence of GFP expression after freeze-thawing and culture

123

5.4 Discussion

125

5.4.1 DQAsome cytotoxicity

125

5.4.2 Mitochondrial internalization of pmtGFP

125

5.4.3 Mitochondrial GFP expression observations

127

5.4.4 Mitochondrial preservation of exogenous DNA

129

5.5 Conclusions

130

Chapter 6. Liposome-mediated mitochondrial DNA transfection of
preimplantation embryo
132
6.1 Introduction

132

6.2 Materials and Methods

133

6.2.1 Mouse embryos

133

6.2.2 Transfection reagents

133

6.2.2.1 Plasmid vectors

133

6.2.2.2 Liposome and lipoplex

134

6.2.3 Transfection assays

134

6.2.3.1 Nuclear transfection

134

6.2.3.2 Mitochondrial transfection

134

6.2.4 Assessment of transfection efficiency
6.2.4.1 Preparation of embryo lysates for PCR analysis

135
135

viii

6.2.4.2 PCR assay for pmtGFP internalization detection

135

6.2.4.3 RT-PCR for mtgfp transcription

136

6.2.4.4 Microscopic observations

136
137

6.3 Results
6.3.1 Nuclear transfection of murine embryonic cells

137

6.3.1.1 Embryo development

137

6.3.1.2 Expression of pDsRed1Mito

137

6.3.2 DQAsome-mediated DNA transfer into mouse embryos

140

6.3.2.1 Embryo development

140

6.3.2.2 Detection of mtgfp by PCR

145

6.3.2.3 Expression of mtgfp

145

6.3.2.4 RT PCR for mtgfp transcription

151

6.4 Discussion

152

6.4.1 Nuclear transfection at embryonic stage

152

6.4.2 Mitochondrial reconstruction at embryonic stage

153
154

6.5 Conclusions

Chapter 7. Transferring genetically modified mitochondria from one
cell to another: towards the generation of new animal
models
155
7.1 Introduction

155

7.2 Materials and Methods

156

7.2.1 Cell culture

156

7.2.1.1 Mouse embryonic stem cells

156

7.2.1.2 Mouse fetal neuronal stem (mFNS) cells

157

7.2.1.2.1 Generation of mFNS cells
7.2.1.2.2 Cryopreservation and thawing of mFNS cells

157
159

7.2.1.3 Rat fetal fibroblast cells

159

7.2.1.4 Bovine fibroblast cells

159

7.2.1.5 Human kidney 293 cells

160

7.2.2 Transfection of cultured mammalian cells

160

7.2.3 Assessment of transfection efficiency

161

7.2.3.1 Microscopic observations

161

7.2.3.2 Flow cytometry analysis

161

ix

7.2.4 Nuclear transfer/cytofusion procedures

161

7.2.4.1 Generation of donor cells

161

7.2.4.1.1 Mouse fetal neuronal stem cells generation
161
7.2.4.1.2 Cell sorting
162
7.2.4.1.3 Preparation of cells for micromanipulation and handmade cloning (HMC)
162
7.2.4.2 Preparation of recipient cells
7.2.4.2.1 Mouse oocytes
7.2.4.2.2 Bovine oocytes
7.2.4.3 Micromanipulation
7.2.4.3.1 Nuclear transfer
7.2.4.3.2 Cell injection
7.2.4.4 Hand-made cloning (HMC)/cytofusion
7.2.4.4.1 Preparation of demi-oocytes
7.2.4.4.2 Reconstruction of nuclear transfer embryos
7.2.4.4.3 Cytofusion to generate tetraploid embryos
7.2.4.4.4 Embryo culture
7.2.4.5 Assessment of reconstructed embryos
7.2.4.5.1 Embryo development
7.2.4.5.2 Epifluorescence observations
7.2.4.5.3 PCR analysis
7.3 Results

163
163
163
164
164
165
165
165
166
167
167
168
168
168
168
169

7.3.1 Mitochondrial transfection in differentmammalian cell types

169

7.3.2 Transferring GFP positive mFNS cells into eggs/embryos

173

7.3.2.1 pmtGFP transfected mFNS cell as donor cells

173

7.3.2.2 Nuclear transfer embryos generated by micromanipulation

173

7.3.2.3 Eggs/embryos injected with mFNS cells

175

7.3.2.4 Nuclear transfer embryos generated by HMC

178

7.3.2.5 HMC fusion of mFNS cells with oocyte karyoplast

178

7.4 Discussion

181

7.4.1 Mitochondrial transfection in mammalian cells

181

7.4.1.1 DQAsome mitochondrial transfection
7.4.1.2 Mitochondrial expression of mtgfp
7.4.1.3 Mitochondrial transfection of pmtGFP in OKO
ES cells
7.4.2 Embryos carrying reconstructed mitochondria

181
182
183
184

x

7.4.2.1 The generation of donor cell with modified
mitochondria
7.4.2.2 Survival rate and embryo development
7.4.2.3 The fate of pmtGFP following cell transfer
7.5 Conclusions

Chapter 8. General Discussion

184
185
187
190

191

8.1 A new mitochondrial DNA delivery system

191

8.2 The minimitochondrial genome pmtGFP

192

8.3 Future applications of minimitochondrial genome

193

8.4 Mitochondrial reconstruction in embryos

194

8.5 Concluding remarks

196

References

197

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