The Human Mitochondrial Genome: From Basic Biology to Disease

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The Human Mitochondrial Genome: From Basic Biology to Disease
Copyright
Dedication
Contents
	Part 1 Biology of human mtDNA1
	Part 2 mtDNA evolution and exploitation109
	Part 3 mtDNA mutations171
	Part 4 mtDNA-determined diseases and therapies351
List of Contributors
Editor’s biographies
Preface
	References
Acknowledgments
Part 1: Biology of human mtDNA
1 mtDNA replication, maintenance, and nucleoid organization
	1.1 Human mitochondrial DNA
		1.1.1 Characteristics of mitochondrial DNA
		1.1.2 Organization of the human mitochondrial genome
	1.2 The process of mtDNA replication
		1.2.1 Replication mechanisms
		1.2.2 Priming
		1.2.3 Elongation of mtDNA replication
			1.2.3.1 The mitochondrial DNA polymerase POL γ
			1.2.3.2 The mitochondrial DNA helicase Twinkle
			1.2.3.3 The mitochondrial single-stranded DNA-binding protein
			1.2.3.4 The mitochondrial DNA replisome
		1.2.4 Termination of mtDNA replication
			1.2.4.1 Primer removal
			1.2.4.2 Ligation
			1.2.4.3 Separation
		1.2.5 Other proteins involved in mtDNA replication
	1.3 The mitochondrial dNTP supply
	1.4 Mitochondrial nucleoids
		1.4.1 Nucleoid composition
			1.4.1.1 mtDNA
			1.4.1.2 Nucleoid-associated proteins
		1.4.2 Nucleoid topology
		1.4.3 Nucleoid localization
		1.4.4 Nucleoid segregation
	Acknowledgments
	References
2 Human mitochondrial transcription and translation
	2.1 Introduction
	2.2 Coordination of mitochondrial DNA replication and transcription
		2.2.1 Overview of mitochondrial DNA replication
		2.2.2 The mitochondrial DNA control region
			2.2.2.1 The mitochondrial displacement loop
			2.2.2.2 The switch between replication and transcription
	2.3 Mitochondrial transcription and mitochondrial RNA transactions
		2.3.1 Mitochondrial DNA transcription
			2.3.1.1 Transcription initiation
			2.3.1.2 Transcription elongation
			2.3.1.3 Transcription termination
		2.3.2 The mitochondrial transcriptome
		2.3.3 Mitochondrial RNA-binding proteins and RNA biology
			2.3.3.1 Mitochondrial RNA processing
			2.3.3.2 Mitochondrial RNA maturation
			2.3.3.3 Mitochondrial RNA chaperones and mRNA stability
			2.3.3.4 Mitochondrial RNA translation activators
	2.4 Mitochondrial translation
		2.4.1 The mitochondrial translation machinery
			2.4.1.1 Mitoribosome structure
			2.4.1.2 Mitoribosome biogenesis
		2.4.2 Mitochondrial protein synthesis
			2.4.2.1 Mitochondrial translation initiation
			2.4.2.2 Mitochondrial translation elongation
			2.4.2.3 Mitochondrial translation termination and mitoribosome recycling
			2.4.2.4 Cotranslational membrane insertion of newly synthesized polypeptides
	2.5 Compartmentalization of gene expression
		2.5.1 Mitochondrial DNA nucleoids
		2.5.2 Mitochondrial RNA granules
		2.5.3 Mitochondrial RNA degradosome
	References
3 Epigenetic features of mitochondrial DNA
	3.1 A brief overview of mitochondrial DNA
	3.2 Does cytosine methylation occur in mtDNA?
	3.3 Bisulfite sequencing analysis of mtDNA
	3.4 Estimation of mtDNA methylation with McrBC endonuclease
	3.5 Investigation of 5mC in mtDNA by nucleoside liquid chromatography/mass spectrometry
	3.6 Epigenetic features of mammalian mtDNA
	Acknowledgments
	References
4 Heredity and segregation of mtDNA
	4.1 Introduction
	4.2 General principles of mtDNA segregation
	4.3 Uniparental maternal inheritance of mitochondrial DNA
	4.4 Paternal leakage during mtDNA inheritance
	4.5 mtDNA mutations—homoplasmy versus heteroplasmy
	4.6 Germline segregation of mtDNA mutations and the genetic bottleneck
	4.7 Purifying selection against mtDNA mutations in the germline
	4.8 Somatic mtDNA mutations and clonal expansion
	4.9 Conclusions
	References
Part 2: mtDNA evolution and exploitation
5 Haplogroups and the history of human evolution through mtDNA
	5.1 Early restriction fragment length polymorphism studies
	5.2 The advent of polymerase chain reaction in the mtDNA world
	5.3 Haplogroup nomenclature of human mtDNA
	5.4 The survey of entire mitogenomes
	5.5 The “Out of Africa Exit”
	5.6 The first peopling of the Americas
	5.7 The peopling of an island in the Mediterranean Sea
	References
6 Human nuclear mitochondrial sequences (NumtS)
	6.1 NumtS definition and introduction
	6.2 NumtS discovery
	6.3 NumtS detection
		6.3.1 In silico human NumtS detection based on reference genomes
		6.3.2 Detection of sample-specific NumtS
		6.3.3 In vitro NumtS identification
	6.4 Numtogenesis: Mechanisms of NumtS insertion
	6.5 NumtS variability and polymorphisms
	6.6 The role of NumtS in mtDNA sequencing and disease
	6.7 NumtS annotation: Current and future roles of NumtS
	References
7 mtDNA exploitation in forensics
	7.1 Introduction
	7.2 mtDNA typing in historical forensic identification
	7.3 mtDNA sequencing in forensic practice
		7.3.1 Extraction
		7.3.2 mtDNA quantification by real-time PCR
		7.3.3 Targeted region and PCR amplification
		7.3.4 mtDNA sequencing
		7.3.5 Rapid screening assay for mtDNA type
		7.3.6 Massive parallel sequencing of full mitochondrial genome
	7.4 Data analysis, alignment, and haplotype notation
		7.4.1 Alignment
		7.4.2 Notation for forensics purposes
		7.4.3 Heteroplasmy
	7.5 Interpretation of mtDNA results
		7.5.1 Sequence comparison
		7.5.2 Statistical evaluation: weight of evidence
	7.6 Mitochondrial DNA population databases used in forensics
	7.7 Guidelines and recommendations
	References
Part 3: mtDNA mutations
8 Human mitochondrial DNA repair
	8.1 Base excision repair
	8.2 Repair of bulky lesions
	8.3 Double-strand break repair
	8.4 Mismatch repair
	8.5 Translesion synthesis
	8.6 Concluding remarks
	References
9 Mechanisms of onset and accumulation of mtDNA mutations
	9.1 Mitochondrial DNA abnormalities
		9.1.1 Primary mitochondrial DNA mutants
			9.1.1.1 Rearrangements: deletions and duplications
			9.1.1.2 Mitochondrial DNA point mutants
	9.2 Criteria to designate a primary mtDNA mutation as pathological
	9.3 Clinical and biochemical correlates
	9.4 Mitochondrial genetic rules
	9.5 Selection and counterselection of deleterious mtDNA variants
		9.5.1 Phenotypic selection of fully functional mtDNAs
		9.5.2 Propagation of dysfunctional mitochondria—misuse of the natural process of coupling mitochondrial mass to energy demand
		9.5.3 Selfish mechanisms
		9.5.4 Metabolic configuration and nutrient availability
	9.6 Genetic drift
	9.7 Mitochondrial DNA selection—more or less?
	9.8 Stable heteroplasmy—the persistence of a fixed proportion of mutant and wild-type mtDNA
	9.9 Mitochondrial DNA maintenance disorders
	9.10 Ribonucleotide incorporation—a new mtDNA abnormality and a potential precursor or mitigator of mtDNA deletions and dep...
	9.11 Overlaps between nuclear defects in the mtDNA maintenance system and primary mtDNA mutants
	9.12 A mitochondrial DNA network and its implications for heteroplasmy
	Acknowledgments
	References
10 Mitochondrial DNA mutations and aging
	10.1 Introduction
	10.2 Old and new mitochondrial theories of aging—how changes in mtDNA contribute to aging?
	10.3 Mitochondrial genetics from the perspective of aging
	10.4 mtDNA deletions and aging
		10.4.1 The origin of mtDNA deletions
		10.4.2 How do mtDNA deletions expand during aging?
		10.4.3 Do mtDNA deletions play a role in aging?
	10.5 mtDNA point mutations
		10.5.1 MtDNA point mutations occur during aging
		10.5.2 The origin of somatic mtDNA point mutations during aging: oxidative stress versus replication errors?
		10.5.3 Oxidative damage
		10.5.4 DNA polymerases
		10.5.5 Is mtDNA susceptible to oxidative damage?
		10.5.6 Origin of mtDNA mutations—evidence from animal models
		10.5.7 When are point mutations generated, and how do they expand?
	10.6 How do somatic mtDNA mutations lead to aging?
		10.6.1 Tissue-specific consequences of mtDNA mutations during aging
	10.7 mtDNA mutations and aging of stem cells
	10.8 Conclusions
	Acknowledgments
	References
11 Methods for the identification of mitochondrial DNA variants
	11.1 Introduction to human mtDNA variants detection
	11.2 Techniques for detecting mitochondrial variants
		11.2.1 Polymerase chain reaction–based methods and mtDNA rearrangements detection
			11.2.1.1 Polymerase chain reaction restriction fragment length polymorphism
			11.2.1.2 Southern blotting and long-range polymerase chain reaction
			11.2.1.3 Pyrosequencing
			11.2.1.4 Quantitative polymerase chain reaction
			11.2.1.5 Single molecule–based detection techniques
		11.2.2 Broad-spectrum techniques for detection of variants in whole mtDNA genomes
			11.2.2.1 Single-strand conformation polymorphism
			11.2.2.2 Denaturing high-performance liquid chromatography
			11.2.2.3 Sanger sequencing
			11.2.2.4 Microarrays
			11.2.2.5 Second-generation sequencing
			11.2.2.6 Third-generation sequencing
	11.3 Challenges in mitochondrial variant studies
		11.3.1 Mitochondrial DNA isolation
		11.3.2 NumtS contamination
	11.4 Bioinformatics strategies to detect mitochondrial variants and heteroplasmy
		11.4.1 Reads mapping and genome assembly
		11.4.2 Mitochondrial variant calling
		11.4.3 Mitochondrial phylogenetic analysis
	References
12 Bioinformatics resources, databases, and tools for human mtDNA
	12.1 Introduction to human mtDNA variability (Wallace DC and Attimonelli M)
	12.2 Human mtDNA genomes and variants
		12.2.1 Primary databases: GenBank/ENA/DDBJ (Attimonelli M)
		12.2.2 MITOMAP (Lott MT, Procaccio V, and Zhang S)
			12.2.2.1 Variant status in MITOMAP
			12.2.2.2 Haplogroup assignment in MITOMAP
			12.2.2.3 Allele search function in MITOMAP
			12.2.2.4 Analyzing mtDNA variability using MITOMASTER
			12.2.2.5 MitoTIP
	12.3 The Human MitoCompendium: HmtDB, HmtVar, and HmtPhenome (Attimonelli M, Preste R, and Vitale O)
		12.3.1 HmtDB
			12.3.1.1 HmtDB API
		12.3.2 HmtVar (Preste R, Vitale O, and Attimonelli M)
			12.3.2.1 HmtVar variants pathogenicity assessment (Attimonelli M and Vitale O)
		12.3.3 HmtPhenome (Preste R and Attimonelli M)
	12.4 MSeqDR—Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium (Lott M)
		12.4.1 MvTool
	12.5 Other specialized human mitochondrial databases (Attimonelli M and Preste R)
	12.6 Tools for variant annotations (Attimonelli M and Preste R)
		12.6.1 HmtNote
		12.6.2 HaploGrep
		12.6.3 MitImpact3D
		12.6.4 PON-mt-tRNA [87]
	12.7 Nuclear encoded mitochondrial genes databases (Vitale O and Attimonelli M)
	References
	Further reading
13 Methods and models for functional studies on mtDNA mutations
	13.1 Introduction
	13.2 Models for the study of mtDNA mutations: in vitro models
		13.2.1 Human primary cell lines
		13.2.2 Cybrids
		13.2.3 Patient-specific induced pluripotent stem cells
		13.2.4 Yeast
	13.3 Animal models
		13.3.1 Caenorhabditis elegans
		13.3.2 Drosophila melanogaster
			13.3.2.1 ATP6 mutant
			13.3.2.2 CoI mutants
			13.3.2.3 ND2 mutants
			13.3.2.4 CoII mutant
		13.3.3 Mice
			13.3.3.1 mtDNA deletions
			13.3.3.2 mt-Co1
			13.3.3.3 mt-Nd6
			13.3.3.4 mt-tK (tRNALys)
			13.3.3.5 mt-tA (tRNAAla)
			13.3.3.6 PolgA
			13.3.3.7 Twnk
			13.3.3.8 Mgme1
	13.4 Methods for assessment of functional defects induced by mtDNA alterations
		13.4.1 OXPHOS complexes activity
			13.4.1.1 Spectrophotometric methods
				13.4.1.1.1 Sample preparation
				13.4.1.1.2 NADH:ubiquinone oxidoreductase activity (CI activity)
				13.4.1.1.3 Succinate:ubiquinone oxidoreductase activity (CII activity)
				13.4.1.1.4 Ubiquinol:cytochrome c oxidoreductase activity (CIII activity)
				13.4.1.1.5 Cytochrome c oxidoreductase activity (CIV activity)
				13.4.1.1.6 NADH:cytochrome c oxidoreductase (CI+III activity)
				13.4.1.1.7 Succinate:cytochrome c oxidoreductase (CII+III activity)
				13.4.1.1.8 Hydrolytic activity of ATP synthase (CV activity)
				13.4.1.1.9 Citrate synthase activity
			13.4.1.2 Immunocapture-based assays
		13.4.2 Oxygen consumption
			13.4.2.1 Classic Clark-type electrode methods
			13.4.2.2 High-resolution respirometry
			13.4.2.3 Microrespirometry on multiwell plate
		13.4.3 Determination of mitochondrial membrane potential
		13.4.4 ATP production
		13.4.5 Reactive oxygen species measurement
		13.4.6 Blue Native Polyacrylamide Gel Electrophoresis
	References
Part 4: mtDNA-determined diseases and therapies
14 Mitochondrial DNA-related diseases associated with single large-scale deletions and point mutations
	14.1 Clinical syndromes of mitochondrial DNA-related diseases associated with single large-scale deletions and point mutations
		14.1.1 Exercise intolerance
		14.1.2 Kearns-Sayre syndrome
		14.1.3 Leber-dystonia
		14.1.4 Leber hereditary optic neuropathy
		14.1.5 Maternally inherited diabetes and deafness
		14.1.6 Maternally inherited Leigh syndrome
		14.1.7 Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes
		14.1.8 Mitochondrial myopathy and cardiomyopathy
		14.1.9 Myoclonic epilepsy with ragged red fibers
		14.1.10 Neurogenic muscle weakness, ataxia, retinitis pigmentosa
		14.1.11 Nonsyndromic sensorineural hearing loss
		14.1.12 Pearson marrow pancreas syndrome
		14.1.13 Progressive external ophthalmoplegia/progressive external ophthalmoplegia plus
		14.1.14 Reversible infantile mitochondrial myopathy
	14.2 Molecular genetics of mitochondrial DNA single large-scale deletions and point mutations
	14.3 Diagnostic approach to mitochondrial DNA-related diseases associated with single large-scale deletions and point mutations
		14.3.1 Laboratory tests
		14.3.2 Neuroimaging
		14.3.3 Skeletal muscle histochemistry, electron microscopy, and respiratory chain biochemistry
		14.3.4 Genetic testing
	14.4 Management of mitochondrial DNA-related diseases associated with single large-scale deletions and point mutations
		14.4.1 Supportive therapies
		14.4.2 Vitamins and cofactors
		14.4.3 Emerging therapies
		14.4.4 Reproductive options
	Acknowledgments
	References
15 Nuclear genetic disorders of mitochondrial DNA gene expression
	15.1 Introduction
	15.2 Mechanisms of mtDNA replication
	15.3 Defects of mtDNA replication
		15.3.1 Mutations in POLG
		15.3.2 Mutations in TWNK
		15.3.3 Mutations in DNA2
		15.3.4 Mutations in MGME1
	15.4 Maintenance of dNTP pool
	15.5 Defects of the dNTP salvage pathway and nucleotide metabolism
		15.5.1 Mutations in TK2
		15.5.2 Mutations in RRM2B
		15.5.3 Mutations in MPV17
	15.6 Mechanism of mitochondrial transcription
	15.7 Defects of mitochondrial transcription
		15.7.1 Mutations in TFAM
		15.7.2 Mutations in TFB2M
	15.8 Transcript processing
	15.9 Defects of maturation of pre mt-RNA
		15.9.1 Mutations in RNase P complex (MRPP1, 2, 3)
		15.9.2 Mutations in RNase Z (ELAC2)
	15.10 mt-mRNA maturation and turnover
	15.11 Defects of mt-mRNA maturation and turnover
		15.11.1 Mutations in MTPAP
		15.11.2 Mutations in LRPPRC
	15.12 mt-tRNA maturation
	15.13 Defects of mt-tRNA maturation and modification
		15.13.1 Mutations in TRNT1
		15.13.2 Mutations in PUS1
		15.13.3 Mutations in MTO1 and GTPBP3
		15.13.4 Mutations in TRMU
		15.13.5 Mutations in TRIT1
		15.13.6 Mutations in mitochondrial aminoacyl-tRNA synthetases
	15.14 mt-rRNA maturation
	15.15 Defects of mt-rRNA maturation, modification, and stability
		15.15.1 Mutations in MRM2
		15.15.2 Mutations in FASTKD2
	15.16 Mechanism of mitochondrial translation
	15.17 Mutations in mitoribosomal proteins
	15.18 Defects of translation initiation
		15.18.1 Mutations in MTFMT
		15.18.2 Mutations in RMND1
	15.19 Defects of translation elongation
		15.19.1 Mutations in GFM1
		15.19.2 Mutations in TSFM
	15.20 Defects of translation termination and mitoribosome recycling
		15.20.1 Mutations in C12orf65
		15.20.2 Mutations in GFM2
	15.21 Defects of translational activation and coupling
		15.21.1 Mutations in TACO1
		15.21.2 Mutations in COA3 and C12orf62
	15.22 IMM insertion of mtDNA-encoded OXPHOS proteins
		15.22.1 Mutations in OXA1L
	Acknowledgments
	References
16 mtDNA maintenance: disease and therapy
	16.1 Introduction
	16.2 Defects in mtDNA replisome
	16.3 Defects in mitochondrial nucleotides pool balance
	16.4 Defects in mitochondrial dynamics
	16.5 Defect in nucleoid proteins
	16.6 Experimental therapies
	16.7 General pharmacological approaches
		16.7.1 Targeting mitochondrial biogenesis
		16.7.2 Targeting mTOR pathway
	16.8 Disease-tailored therapies
		16.8.1 Nucleos(t)ide supplementation therapies
		16.8.2 Clearance of toxic metabolites
		16.8.3 Enzyme replacement
		16.8.4 Platelet infusion
		16.8.5 Hematopoietic stem cell transplantation
		16.8.6 Erythrocytes encapsulated thymidine phosphorylase
		16.8.7 Liver transplant: tissue-specific disorder and source of enzyme replacement
		16.8.8 Gene therapy
	Acknowledgments
	References
17 mtDNA mutations in cancer
	17.1 The landscape of mtDNA mutations in cancer
	17.2 Functional effects of mtDNA mutations in solid cancers
		17.2.1 mtDNA mutations and metabolic adaptation
		17.2.2 MtDNA mutations and hypoxic stress
		17.2.3 mtDNA mutations and metastatic progression
	17.3 The fate of severely pathogenic mtDNA mutations in progressing solid tumors
		17.3.1 Molecular mechanisms behind selection and purification of mtDNA mutations in cancer
		17.3.2 Compensatory mechanisms to overcome mitochondrial dysfunction
		17.3.3 MtDNA mutations in oncocytomas: an exception from the rule
	17.4 Clinical potential of cancer-associated mtDNA mutations
		17.4.1 MtDNA mutations and cancer treatment
			17.4.1.1 Chemotherapy
			17.4.1.2 Radiotherapy
			17.4.1.3 Interventions in cancer therapy based on mitochondrial functional status
		17.4.2 Cancer-specific mtDNA mutations as markers of tumor progression
	17.5 Insights from next generation sequencing and bioinformatics approaches
		17.5.1 Technical pitfalls and false discoveries of the past
		17.5.2 Methodological recommendations for mtDNA mutation analysis in the advent of next generation sequencing in oncology
		17.5.3 The influence of big data on what we know on mtDNA mutations in cancer
	References
18 MitoTALENs for mtDNA editing
	18.1 Introduction
	18.2 The use of specific endonucleases to target mtDNA
	18.3 The use of mitoTALENs to target mtDNA
	18.4 Structure of mitoTALENs
	18.5 MitoTALENs targeting mutations in cybrids
	18.6 MitoTALENs in a heteroplasmic mouse model carrying a tRNAAla mutation
	18.7 MitoTALENs and induced pluripotent stem cells
	18.8 Other uses of mitoTALENs
		18.8.1 MitoTALENs in germline transmission
			18.8.1.1 MitoTALENs to study mtDNA replication
		18.8.2 MitoTevTAL nuclease
	18.9 Pros and cons of using mitoTALENs for gene therapy
		18.9.1 Specificity and mtDNA depletion
		18.9.2 Off-target sequences in the nucleus
		18.9.3 Easy design of new recognition sites
		18.9.4 MitoTALEN gene size
		18.9.5 The future of mitoTALENs as therapy
	References
19 Mitochondrially targeted zinc finger nucleases
	19.1 Introduction
	19.2 Zinc finger domain—structure and interaction with DNA
	19.3 Designer zinc fingers
	19.4 Chimeric zinc finger proteins—birth of zinc finger nuclease
	19.5 Manipulation of the mammalian mitochondrial genome with mtZFNs
		19.5.1 The first step
		19.5.2 In vivo use of mtZFNs
	19.6 Concluding remarks
	Acknowledgments
	References
20 Mitochondrial movement between mammalian cells: an emerging physiological phenomenon
	20.1 Introduction
	20.2 Cell-to-cell transfer of mitochondria with mtDNA: a brief overview
	20.3 Translational benefits of mitochondrial transfer
		20.3.1 Mitochondrial transfer between cells
			20.3.1.1 Mitochondrial transfer into tumor cells
			20.3.1.2 Mitochondrial transfer into normal cells
			20.3.1.3 Mitochondrial donation therapy to prevent mitochondrial diseases in offspring
		20.3.2 Transfer of isolated mitochondria
			20.3.2.1 Ischemic heart disease
			20.3.2.2 Neurodegenerative disorders and ischemic stroke
			20.3.2.3 Behavioral disorders
			20.3.2.4 Cancer sensitization to treatment
	20.4 Mechanisms of mitochondrial transfer
	20.5 Mito-nuclear crosstalk: potential consequences of mitochondrial transfer/transplantation
	20.6 Concluding statement
	Acknowledgments
	References
Index
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