Human mitochondrial DNA
Human mitochondrial DNA with the 37 genes on their respective H- and
Electron microscopy reveals mitochondrial
DNA in discrete foci. Bars:
200 nm. (A) Cytoplasmic section after immunogold labelling with
anti-DNA; gold particles marking mt
DNA are found near the
mitochondrial membrane (black dots in upper right). (B) Whole mount
view of cytoplasm after extraction with CSK buffer and immunogold
labelling with anti-DNA; mt
DNA (marked by gold particles) resists
extraction. From Iborra et al., 2004.
DNA or mDNA) is the
DNA located in
mitochondria, cellular organelles within eukaryotic cells that convert
chemical energy from food into a form that cells can use, adenosine
triphosphate (ATP). Mitochondrial
DNA is only a small portion of the
DNA in a eukaryotic cell; most of the
DNA can be found in the cell
nucleus and, in plants and algae, also in plastids such as
In humans, the 16,569 base pairs of mitochondrial
DNA encode for only
Human mitochondrial DNA
Human mitochondrial DNA was the first significant part of
the human genome to be sequenced. In most species, including humans,
DNA is inherited solely from the mother.
Since animal mt
DNA evolves faster than nuclear genetic
markers, it represents a mainstay of phylogenetics and
evolutionary biology. It also permits an examination of the
relatedness of populations, and so has become important in
anthropology and biogeography.
2 Mitochondrial inheritance
2.1 Female inheritance
2.2 The mitochondrial bottleneck
2.3 Male inheritance
2.4 Mitochondrial donation
3.1 Circular versus linear
3.2 In mammals
3.3 In plants
3.4 In protists
4 Genome diversity
4.2 Plants and fungi
7 Mutations and disease
7.2 Genetic illness
7.3 Use in disease diagnosis
7.4 Relationship with aging
7.5 Correlation of the mt
DNA base composition with animals lifespan
7.6 Relationship with non-B (non-canonical)
8 Use in identification
10 Mitochondrial sequence databases
11 Mitochondrial mutation databases
12 See also
14 External links
Nuclear and mitochondrial
DNA are thought to be of separate
evolutionary origin, with the mt
DNA being derived from the circular
genomes of the bacteria that were engulfed by the early ancestors of
today's eukaryotic cells. This theory is called the endosymbiotic
theory. Each mitochondrion is estimated to contain 2–10 mtDNA
copies. In the cells of extant organisms, the vast majority of the
proteins present in the mitochondria (numbering approximately 1500
different types in mammals) are coded for by nuclear DNA, but the
genes for some, if not most, of them are thought to have originally
been of bacterial origin, having since been transferred to the
eukaryotic nucleus during evolution.
The reasons why mitochondria have retained some genes are debated. The
existence in some species of mitochondrion-derived organelles lacking
a genome suggests that complete gene loss is possible, and
transferring mitochondrial genes to the nucleus has several
advantages. The difficulty of targeting remotely-produced
hydrophobic protein products to the mitochondrion is one hypothesis
for why some genes are retained in mtDNA; colocalisation for redox
regulation is another, citing the desirability of localised control
over mitochondrial machinery. Recent analysis of a wide range of
DNA genomes suggests that both these features may dictate
mitochondrial gene retention.
In most multicellular organisms, mt
DNA is inherited from the mother
(maternally inherited). Mechanisms for this include simple dilution
(an egg contains on average 200,000 mt
DNA molecules, whereas a healthy
human sperm was reported to contain on average 5 molecules ),
degradation of sperm mt
DNA in the male genital tract, in the
fertilized egg, and, at least in a few organisms, failure of sperm
DNA to enter the egg. Whatever the mechanism, this single parent
(uniparental inheritance) pattern of mt
DNA inheritance is found in
most animals, most plants and in fungi as well.
In sexual reproduction, mitochondria are normally inherited
exclusively from the mother; the mitochondria in mammalian sperm are
usually destroyed by the egg cell after fertilization. Also, most
mitochondria are present at the base of the sperm's tail, which is
used for propelling the sperm cells; sometimes the tail is lost during
fertilization. In 1999 it was reported that paternal sperm
mitochondria (containing mtDNA) are marked with ubiquitin to select
them for later destruction inside the embryo. Some in vitro
fertilization techniques, particularly injecting a sperm into an
oocyte, may interfere with this.
The fact that mitochondrial
DNA is maternally inherited enables
genealogical researchers to trace maternal lineage far back in time.
(Y-chromosomal DNA, paternally inherited, is used in an analogous way
to determine the patrilineal history.) This is usually accomplished on
DNA by sequencing the hypervariable control
regions (HVR1 or HVR2), and sometimes the complete molecule of the
mitochondrial DNA, as a genealogical
DNA test. HVR1, for example,
consists of about 440 base pairs. These 440 base pairs are then
compared to the control regions of other individuals (either specific
people or subjects in a database) to determine maternal lineage. Most
often, the comparison is made to the revised Cambridge Reference
Sequence. Vilà et al. have published studies tracing the matrilineal
descent of domestic dogs to wolves. The concept of the
Mitochondrial Eve is based on the same type of analysis, attempting to
discover the origin of humanity by tracking the lineage back in time.
DNA is highly conserved, and its relatively slow mutation rates
(compared to other
DNA regions such as microsatellites) make it useful
for studying the evolutionary relationships—phylogeny—of
organisms. Biologists can determine and then compare mt
among different species and use the comparisons to build an
evolutionary tree for the species examined. However, due to the slow
mutation rates it experiences, it is often hard to distinguish between
closely related species to any large degree, so other methods of
analysis must be used.
The mitochondrial bottleneck
Entities undergoing uniparental inheritance and with little to no
recombination may be expected to be subject to Muller's ratchet, the
accumulation of deleterious mutations until functionality is lost.
Animal populations of mitochondria avoid this buildup through a
developmental process known as the mt
DNA bottleneck. The bottleneck
exploits stochastic processes in the cell to increase in the
cell-to-cell variability in mutant load as an organism develops: a
single egg cell with some proportion of mutant mt
DNA thus produces an
embryo where different cells have different mutant loads. Cell-level
selection may then act to remove those cells with more mutant mtDNA,
leading to a stabilisation or reduction in mutant load between
generations. The mechanism underlying the bottleneck is
debated, with a recent mathematical and experimental
metastudy providing evidence for a combination of random partitioning
of mtDNAs at cell divisions and random turnover of mt
within the cell.
Main article: Paternal mt
Doubly uniparental inheritance of mt
DNA is observed in bivalve
mollusks. In those species, females have only one type of mt
whereas males have F type mt
DNA in their somatic cells, but M type of
DNA (which can be as much as 30% divergent) in germline cells.
Paternally inherited mitochondria have additionally been reported in
some insects such as fruit flies, honeybees, and
Male mitochondrial inheritance was recently discovered in Plymouth
Rock chickens. Evidence supports rare instances of male
mitochondrial inheritance in some mammals as well. Specifically,
documented occurrences exist for mice, where the
male-inherited mitochondria were subsequently rejected. It has also
been found in sheep, and in cloned cattle. It has been found
in a single case in a human male.
Although many of these cases involve cloned embryos or subsequent
rejection of the paternal mitochondria, others document in vivo
inheritance and persistence under lab conditions.
Main article: Mitochondrial donation
An IVF technique known as mitochondrial donation or mitochondrial
replacement therapy (MRT) results in offspring containing mt
DNA from a
donor female, and nuclear
DNA from the mother and father. In the
spindle transfer procedure, the nucleus of an egg is inserted into the
cytoplasm of an egg from a donor female which has had its nucleus
removed, but still contains the donor female's mtDNA. The composite
egg is then fertilized with the male's sperm. The procedure is used
when a woman with genetically defective mitochondria wishes to
procreate and produce offspring with healthy mitochondria. The
first known child to be born as a result of mitochondrial donation was
a boy born to a Jordanian couple in Mexico on 6 April 2016.
Circular versus linear
In most multicellular organisms, the mt
DNA – or mitogenome – is
organized as a circular, covalently closed, double-stranded DNA. But
in many unicellular (e.g. the ciliate
Tetrahymena or the green alga
Chlamydomonas reinhardtii) and in rare cases also in multicellular
organisms (e.g. in some species of
Cnidaria ) the mt
DNA is found as
linearly organized DNA. Most of these linear mtDNAs possess telomerase
independent telomeres (i.e. the ends of the linear DNA) with different
modes of replication, which have made them interesting objects of
research, as many of these unicellular organisms with linear mt
For human mitochondrial
DNA (and probably for that of metazoans in
general), 100–10,000 separate copies of mt
DNA are usually present
per somatic cell (egg and sperm cells are exceptions). In mammals,
each double-stranded circular mt
DNA molecule consists of
15,000–17,000 base pairs. The two strands of mt
differentiated by their nucleotide content, with a guanine-rich strand
referred to as the heavy strand (or H-strand) and a cytosine-rich
strand referred to as the light strand (or L-strand). The heavy strand
encodes 28 genes, and the light strand encodes 9 genes for a total of
37 genes. Of the 37 genes, 13 are for proteins (polypeptides), 22
are for transfer
RNA (tRNA) and two are for the small and large
subunits of ribosomal
RNA (rRNA). The human mitogenome contains
overlapping genes (ATP8 and ATP6 as well as ND4L and ND4: see the
human mitochondrial genome map), a feature that is rare in animal
genomes. The 37-gene pattern is also seen among most
metazoans, although in some cases one or more of these genes is absent
and the mt
DNA size range is greater.
The 37 genes of the
Cambridge Reference Sequence
Cambridge Reference Sequence for human
DNA and their locations
in the mitogenome
ATP synthase, Fo subunit 8 (complex V)
08,366–08,572 (overlap with MT-ATP6)
ATP synthase, Fo subunit 6 (complex V)
08,527–09,207 (overlap with MT-ATP8)
Cytochrome c oxidase, subunit 1 (complex IV)
Cytochrome c oxidase, subunit 2 (complex IV)
Cytochrome c oxidase, subunit 3 (complex IV)
Cytochrome b (complex III)
NADH dehydrogenase, subunit 1 (complex I)
NADH dehydrogenase, subunit 2 (complex I)
NADH dehydrogenase, subunit 3 (complex I)
NADH dehydrogenase, subunit 4L (complex I)
10,470–10,766 (overlap with MT-ND4)
NADH dehydrogenase, subunit 4 (complex I)
10,760–12,137 (overlap with MT-ND4L)
NADH dehydrogenase, subunit 5 (complex I)
NADH dehydrogenase, subunit 6 (complex I)
Alanine (Ala or A)
Arginine (Arg or R)
Asparagine (Asn or N)
Aspartic acid (Asp or D)
Cysteine (Cys or C)
Glutamic acid (Glu or E)
Glutamine (Gln or Q)
Glycine (Gly or G)
Histidine (His or H)
Isoleucine (Ile or I)
Leucine (Leu-UUR or L)
Leucine (Leu-CUN or L)
Lysine (Lys or K)
Methionine (Met or M)
Phenylalanine (Phe or F)
Proline (Pro or P)
Serine (Ser-UCN or S)
Serine (Ser-AGY or S)
Threonine (Thr or T)
Tryptophan (Trp or W)
Tyrosine (Tyr or Y)
Valine (Val or V)
Small subunit : SSU (12S)
Large subunit : LSU (16S)
Great variation in mt
DNA gene content and size exists among fungi and
plants, although there appears to be a core subset of genes that are
present in all eukaryotes (except for the few that have no
mitochondria at all). Some plant species have enormous
mitochondrial genomes, with
Silene conica mt
DNA containing as many as
11,300,000 base pairs. Surprisingly, even those huge mtDNAs
contain the same number and kinds of genes as related plants with much
smaller mtDNAs. The genome of the mitochondrion of the cucumber
(Cucumis sativus) consists of three circular chromosomes (lengths
1556, 84 and 45 kilobases), which are entirely or largely autonomous
with regard to their replication.
The smallest mitochondrial genome sequenced to date is the 5967 bp
DNA of the parasite Plasmodium falciparum.
There are six main genome types found in mitochondrial genomes,
classified by their structure (e.g. circular versus linear), size,
presence of introns or plasmid like structures, and whether the
genetic material is a singular molecule or collection of homogeneous
or heterogeneous molecules.
There is only one mitochondrial genome type found in animal cells.
This genome usually contains one circular molecule with between
11–28kbp of genetic material (type 1).
Plants and fungi
There are three different genome types found in plants and fungi. The
first type is a circular genome that has introns (type 2) and may
range from 19–1000kbp in length. The second genome type is a
circular genome (about 20–1000kbp) that also has a plasmid-like
structure (1kb) (type 3). The final genome type that can be found in
plant and fungi is a linear genome made up of homogeneous DNA
molecules (type 5).
Protists contain the most diverse mitochondrial genomes, with five
different types found in this kingdom. Type 2, type 3 and type 5
mentioned in the plant and fungal genomes also exists in some protist,
as well as two unique genome types. The first of these is a
heterogeneous collection of circular
DNA molecules (type 4) and the
final genome type found in protists is a heterogeneous collection of
linear molecules (type 6). Genome types 4 and 6 both range from
1–200kbp in size.
Endosymbiotic gene transfer, the process of genes that were coded in
the mitochondrial genome being transferred to the cell's main genome
likely explains why more complex organisms, such as humans, have
smaller mitochondrial genomes than simpler organisms, such as
Fungi, Plant, Protista
Fungi, Plant, Protista
Large molecule and small plasmid like structures
Heterogeneous group of molecules
Fungi, Plant, Protista
Homogeneous group of molecules
Heterogeneous group of molecules
DNA is replicated by the
DNA polymerase gamma complex
which is composed of a 140 kDa catalytic
DNA polymerase encoded by the
POLG gene and two 55 kDa accessory subunits encoded by the POLG2
gene. The replisome machinery is formed by
DNA polymerase, TWINKLE
and mitochondrial SSB proteins. TWINKLE is a helicase, which unwinds
short stretches of ds
DNA in the 5′ to 3′ direction.
During embryogenesis, replication of mt
DNA is strictly down-regulated
from the fertilized oocyte through the preimplantation embryo. The
resulting reduction in per-cell copy number of mt
DNA plays a role in
the mitochondrial bottleneck, exploiting cell-to-cell variability to
ameliorate the inheritance of damaging mutations. At the
blastocyst stage, the onset of mt
DNA replication is specific to the
cells of the trophectoderm. In contrast, the cells of the inner
cell mass restrict mt
DNA replication until they receive the signals to
differentiate to specific cell types.
In animal mitochondria, each
DNA strand is transcribed continuously
and produces a polycistronic
RNA molecule. Between most (but not all)
protein-coding regions, tRNAs are present (see the human mitochondrial
genome map). During transcription, the tRNAs acquire their
characteristic L-shape that gets recognized and cleaved by specific
enzymes. With the mitochondrial
RNA processing, individual mRNA, rRNA,
RNA sequences are released from the primary transcript.
Folded tRNAs therefore act as secondary structure punctuations.
Mutations and disease
Human mitochondrial DNA
Human mitochondrial DNA with groups of protein-, rRNA- and
The involvement of mitochondrial
DNA in several human diseases.
The concept that mt
DNA is particularly susceptible to reactive oxygen
species generated by the respiratory chain due to its proximity
remains controversial. mt
DNA does not accumulate any more
oxidative base damage than nuclear DNA. It has been reported that
at least some types of oxidative
DNA damage are repaired more
efficiently in mitochondria than they are in the nucleus. mt
packaged with proteins which appear to be as protective as proteins of
the nuclear chromatin. Moreover, mitochondria evolved a unique
mechanism which maintains mt
DNA integrity through degradation of
excessively damaged genomes followed by replication of intact/repaired
mtDNA. This mechanism is not present in the nucleus and is enabled by
multiple copies of mt
DNA present in mitochondria  The outcome of
mutation in mt
DNA may be an alteration in the coding instructions for
some proteins, which may have an effect on organism metabolism
Further information: Mitochondrial disease
Mutations of mitochondrial
DNA can lead to a number of illnesses
including exercise intolerance and
Kearns–Sayre syndrome (KSS),
which causes a person to lose full function of heart, eye, and muscle
movements. Some evidence suggests that they might be major
contributors to the aging process and age-associated pathologies.
Particularly in the context of disease, the proportion of mutant mtDNA
molecules in a cell is termed heteroplasmy. The within-cell and
between-cell distributions of heteroplasmy dictate the onset and
severity of disease  and are influenced by complicated stochastic
processes within the cell and during development.
Mutations in mitochondrial tRNAs can be responsible for severe
diseases like the MELAS and MERRF syndromes.
Mutations in nuclear genes that encode proteins that mitochondria use
can also contribute to mitochondrial diseases. These diseases do not
follow mitochondrial inheritance patterns, but instead follow
Mendelian inheritance patterns.
Use in disease diagnosis
Recently a mutation in mt
DNA has been used to help diagnose prostate
cancer in patients with negative prostate biopsy.
Relationship with aging
Though the idea is controversial, some evidence suggests a link
between aging and mitochondrial genome dysfunction. In essence,
mutations in mt
DNA upset a careful balance of reactive oxygen species
(ROS) production and enzymatic ROS scavenging (by enzymes like
superoxide dismutase, catalase, glutathione peroxidase and others).
However, some mutations that increase ROS production (e.g., by
reducing antioxidant defenses) in worms increase, rather than
decrease, their longevity. Also, naked mole rats, rodents about
the size of mice, live about eight times longer than mice despite
having reduced, compared to mice, antioxidant defenses and increased
oxidative damage to biomolecules. Once, there was thought to be a
positive feedback loop at work (a 'Vicious Cycle'); as mitochondrial
DNA accumulates genetic damage caused by free radicals, the
mitochondria lose function and leak free radicals into the cytosol. A
decrease in mitochondrial function reduces overall metabolic
efficiency. However, this concept was conclusively disproved when
it was demonstrated that mice, which were genetically altered to
DNA mutations at accelerated rate do age prematurely, but
their tissues do not produce more ROS as predicted by the 'Vicious
Cycle' hypothesis. Supporting a link between longevity and
mitochondrial DNA, some studies have found correlations between
biochemical properties of the mitochondrial
DNA and the longevity of
species. Extensive research is being conducted to further
investigate this link and methods to combat aging. Presently, gene
therapy and nutraceutical supplementation are popular areas of ongoing
research. Bjelakovic et al. analyzed the results of 78 studies
between 1977 and 2012, involving a total of 296,707 participants, and
concluded that antioxidant supplements do not reduce all-cause
mortality nor extend lifespan, while some of them, such as beta
carotene, vitamin E, and higher doses of vitamin A, may actually
Correlation of the mt
DNA base composition with animals lifespan
Animal species mt
DNA base composition was retrieved from the MitoAge
database and compared to their maximum life span from AnAge database.
Over the past decade, an Israeli research group led by Professor Vadim
Fraifeld has shown that extraordinarily strong and significant
correlations exist between the mt
DNA base composition and animal
species-specific maximum life spans. As demonstrated in
their work, higher mt
DNA guanine + cytosine content (GC%) strongly
associates with longer maximum life spans across animal species. An
additional astonishing observation is that the mt
DNA GC% correlation
with the maximum life spans is independent of the well-known
correlation between animal species metabolic rate and maximum life
spans. The mt
DNA GC% and resting metabolic rate explain the
differences in animal species maximum life spans in a multiplicative
manner (i.e., species maximum life span = their mt
DNA GC% * metabolic
rate). To support the scientific community in carrying out
comparative analyses between mt
DNA features and longevity across
animals, a dedicated database was built named MitoAge.
Relationship with non-B (non-canonical)
Deletion breakpoints frequently occur within or near regions showing
non-canonical (non-B) conformations, namely hairpins, cruciforms and
cloverleaf-like elements. Moreover, there is data supporting the
involvement of helix-distorting intrinsically curved regions and long
G-tetrads in eliciting instability events. In addition, higher
breakpoint densities were consistently observed within GC-skewed
regions and in the close vicinity of the degenerate sequence motif
YMMYMNNMMHM. Recently (2017) was found that all mitochodrial
genomes sequenced so far contain many of inverted repeats necessary
DNA formation and these loci are particularly enriched
in replication origin sites, D-loops and stem loops.
Use in identification
For use in human identification, see
Human mitochondrial DNA.
Unlike nuclear DNA, which is inherited from both parents and in which
genes are rearranged in the process of recombination, there is usually
no change in mt
DNA from parent to offspring. Although mt
recombines, it does so with copies of itself within the same
mitochondrion. Because of this and because the mutation rate of animal
DNA is higher than that of nuclear DNA, mt
DNA is a powerful tool
for tracking ancestry through females (matrilineage) and has been used
in this role to track the ancestry of many species back hundreds of
The rapid mutation rate (in animals) makes mt
DNA useful for assessing
genetic relationships of individuals or groups within a species and
also for identifying and quantifying the phylogeny (evolutionary
relationships; see phylogenetics) among different species. To do this,
biologists determine and then compare the mt
DNA sequences from
different individuals or species. Data from the comparisons is used to
construct a network of relationships among the sequences, which
provides an estimate of the relationships among the individuals or
species from which the mtDNAs were taken. mt
DNA can be used to
estimate the relationship between both closely related and distantly
related species. Due to the high mutation rate of mt
DNA in animals,
the 3rd positions of the codons change relatively rapidly, and thus
provide information about the genetic distances among closely related
individuals or species. On the other hand, the substitution rate of
mt-proteins is very low, thus amino acid changes accumulate slowly
(with corresponding slow changes at 1st and 2nd codon positions) and
thus they provide information about the genetic distances of distantly
related species. Statistical models that treat substitution rates
among codon positions separately, can thus be used to simultaneously
estimate phylogenies that contain both closely and distantly related
DNA was admitted into evidence for the first time ever
in 1996 during State of Tennessee v. Paul Ware.
In the 1998 court case of Commonwealth of Pennsylvania v. Patricia
Lynne Rorrer, mitochondrial
DNA was admitted into evidence in the
State of Pennsylvania for the first time. The case was
featured in episode 55 of season 5 of the true crime drama series
Forensic Files (season 5).
DNA was first admitted into evidence in
the successful prosecution of David Westerfield for the 2002
kidnapping and murder of 7-year-old Danielle van Dam in San Diego: it
was used for both human and dog identification. This was the first
trial in the U.S. to admit canine DNA.
The remains of King Richard III were identified by comparing his mtDNA
with that of two matrilineal descendants of his sister.
DNA was discovered in the 1960s by Margit M. K. Nass and
Sylvan Nass by electron microscopy as DNase-sensitive threads inside
mitochondria, and by Ellen Haslbrunner,
Hans Tuppy and Gottfried
Schatz by biochemical assays on highly purified mitochondrial
Mitochondrial sequence databases
Several specialized databases have been founded to collect
mitochondrial genome sequences and other information. Although most of
them focus on sequence data, some of them include phylogenetic or
MitoSatPlant: Mitochondrial microsatellites database of
MitoBreak: the mitochondrial
DNA breakpoints database.
MitoFish and MitoAnnotator: a mitochondrial genome database of
fish. See also Cawthorn et al.
MitoZoa 2.0: a database for comparative and evolutionary analyses of
mitochondrial genomes in Metazoa. (no longer available)
InterMitoBase: an annotated database and analysis platform of
protein-protein interactions for human mitochondria. (apparently
last updated in 2010, but still available)
Mitome: a database for comparative mitochondrial genomics in metazoan
animals (no longer available)
MitoRes: a resource of nuclear-encoded mitochondrial genes and their
products in metazoa (apparently no longer being updated)
Mitochondrial mutation databases
Several specialized databases exist that report polymorphisms and
mutations in the human mitochondrial DNA, together with the assessment
of their pathogenicity.
MITOMAP: A compendium of polymorphisms and mutations in human
MitImpact: A collection of pre-computed pathogenicity predictions for
all nucleotide changes that cause non-synonymous substitutions in
human mitochondrial protein coding genes .
Archaeogenetics of the Near East
Human mitochondrial DNA
Human mitochondrial DNA haplogroup
Human mitochondrial genetics
Single origin theory
Genetic history of Africa
Genetic history of Europe
Genetic history of the British Isles
Genetic history of the Iberian Peninsula
Genetic history of indigenous peoples of the Americas
Genetic history of Italy
Genetic history of North Africa
Genetics and archaeogenetics of South Asia
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