Article

ISSN 0006-2979, Biochemistry (Moscow), 2025, Vol. 90, No. 12, pp. 1919-1928 © The Author(s) 2025. This article is an open access publication.

Published in Russian in Biokhimiya, 2025, Vol. 90, No. 12, pp. 2021-2031.

1919

REVIEW

Mechanisms of Intracellular Selection

of Mitochondrial DNA

Georgii Muravyov

1,2

and Dmitry A. Knorre

2,a

Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University,

119234 Moscow, Russia

A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University,

119234 Moscow, Russia

e-mail: knorre@belozersky.msu.ru

Received September 23, 2025

Revised November 15, 2025

Accepted November 20, 2025

Abstract— Eukaryotic cells contain multiple mitochondrial DNA (mtDNA) molecules. Heteroplasmy is coexis-

tence in the same cell of different mtDNA variants competing for cellular resources required for their repli-

cation. Here, we review documented cases of emergence and spread of selfish mtDNA (i.e., mtDNA that has

a selective advantage in a cell but decreases cell fitness) in eukaryotic species, from humans to baker’s yeast.

The review discusses hypothetical mechanisms enabling preferential proliferation of certain mtDNA variants

in heteroplasmy. We propose that selfish mtDNAs have significantly influenced the evolution of eukaryotes

and may be responsible for the emergence of uniparental inheritance and constraints on the mtDNA copy

number in germline cells.

DOI: 10.1134/S0006297925603296

Keywords: mitochondrial DNA, mtDNA quality control, mitophagy, heteroplasmy, intracellular selection, selfish

gene

* To whom correspondence should be addressed.

INTRODUCTION

Mitochondria are semi-autonomous organelles

with their own genome. Mitochondrial DNA (mtDNA)

has been found in a vast majority of eukaryotes, ex-

cept few species [1]. It encodes proteins necessary

for oxidative phosphorylation, as well as components

of the mitochondrial translation system [2]. Typical-

ly, a single eukaryotic cell contains several mtDNA

copies, although their exact number may depend on

the conditions, cell type, and prior cell history [3-5].

New mtDNA variants appear through mutations.

The state when a cell has several mtDNA variants is

called heteroplasmy [6]. During cell division, mtDNA

molecules are distributed randomly between the

new cells. After several (sometimes, many) genera-

tions, due to random genetic drift, the descendants

of a heteroplasmic cell retain only one of the mtDNA

variants, the state referred to as homoplasmy  [7].

As a result, the emergence of heteroplasmy (due to

mutations or cell fusion) is balanced by random ge-

netic drift in the frequencies of mtDNA mitotypes,

leading to the preservation of one or another mtDNA

mitotype in the cell descendants (Fig. 1).

mtDNA is a subject of natural selection at multi-

ple organizational levels: molecular, organelle, cellu-

lar, or organismal [7]. Therefore, the selection process

can be multidirectional, i.e., the same mtDNA variant

might have a high fitness at one organizational level

and low fitness at another [7]. To describe selection

at the cellular level, it is important to introduce the

concept of mutant mtDNA pathogenicity threshold.

Cell phenotype is a complex function of mtDNA gen-

otypes, as it reflects manifestations of these geno-

types at the levels of transcription, translation, en-

zymatic activity, respiratory chain function, and cell

as a whole. However, when the proportion of mutant

mtDNA variants is less than a certain threshold for

a given heteroplasmic cell, harmful mutations may

not manifest themselves at the cellular or organismal

MURAVYOV, KNORRE1920

BIOCHEMISTRY (Moscow) Vol. 90 No. 12 2025

levels [8, 9], usually indicating an excess number of

mtDNA copies per cell. As a result, mtDNA variants

carrying mutations harmful to the cell and, at the

same time, providing an advantage in fitness at the

intracellular level, can avoid selection in individual

cells until their allele frequency reaches a specific

threshold. Such mutations can persist for a long time

or even gain an advantage in organisms and popula-

tions. Furthermore, in some cases, deleterious mtDNA

mutations harmful to the multicellular organism, may

gain a fitness advantage at the cellular level. This is

exemplified by the spread of colonic crypts contain-

ing cells with mutations in the mitochondrial cyto-

chrome oxidase CO1 gene [10].

mtDNA variants characterized by a high fitness

at the intracellular level but not beneficial (or even

deleterious) to the cell or entire organism fall un-

der the definition of “selfish genetic elements” [11].

In this work, we will refer to such mitotypes (mtDNA

variants) as selfish mtDNA. There have been numer-

ous descriptions of the emergence and spreading of

selfish mtDNA in both nature and artificial experi-

mental systems. In the next section, we discussed ex-

amples of intracellular selection of mtDNA enabling

proliferation of selfish mtDNA.

INTRACELLULAR SELECTION

AND SELFISH mtDNA IN NATURE

AND EXPERIMENTAL SYSTEMS

One evidence of mtDNA selection at the intracel-

lular level is clonal expansion of deletion-containing

mtDNA variants in the cells of postmitotic tissues of

multicellular animals. Clonal expansion is the process

where a mutated mtDNA molecule multiplies within

some cells, leading to a higher concentration of that

specific mtDNA, while in other cells, this mtDNA

variant is absent [12,  13]. Analysis of sequences of

mtDNA control regions in individual human somat-

ic cells has shown that proportion of mutant mtDNA

variants (i.e., those differing from the main mitotype

in a given organism) in some cells can significantly

increase with age [14]. In most cases, it is difficult to

distinguish whether the clonal expansion is caused

random stochastic drift or results from positive intra-

cellular selection. Nonetheless, the mutation patterns

found in individual cells from different tissues dif-

fer markedly, providing suggestive evidence for the

presence of positive intracellular selection. For exam-

ple, it has been shown that in cardiomyocytes, most

de  novo mutations occurred in the mtDNA genome

region with the coordinates 16,025-16,055  bp, where-

as in buccal epithelial cells, this region contained no

mutations [14]. This result suggests that either (1)the

spectrum of mutations varies greatly among differ-

ent tissues or (2) due to the intracellular selection,

some mtDNA variants undergo clonal expansion. Both

these processes – selection and genetic drift – have

been demonstrated in mice with artificially created

heteroplasmy. The animals showed an increase in the

frequency of certain mtDNA variants in some tissues,

but not in others [15]. In another study, sequencing

mtDNA from individual cells of aged (2-year-old) and

young mice revealed mutant mtDNA variants, the

proportion of which increased with age faster than

Fig. 1. Heteroplasmy arises as a result of mtDNA mutations in a cell or via cell fusion with other cells. Over generations,

random drift may cause descendants of the heteroplasmic cells to revert to homoplasmy. Mitochondria are not shown

in this figure, and it is assumed that mtDNAs constitute a single population within each cell.

MECHANISMS OF INTRACELLULAR SELECTION OF MITOCHONDRIAL DNA 1921

BIOCHEMISTRY (Moscow) Vol. 90 No. 12 2025

can be explained by random drift [16]. These muta-

tions, which were under positive selection in somat-

ic cells, were predominantly located in the mtDNA

control region containing the origin of replication.

Interestingly, in some cases, the relative content of

associated passenger mutations also increased [16].

Finally, comparison of frequencies of different

mtDNA variants in mothers and offspring suggested

the presence of both purifying [17, 18] and positive

[19, 20] selection of mtDNAs in mammalian germ-

lines. The direction of selection largely depends on

the frequencies of mtDNA alleles in germline cells

and specific mtDNA mitotypes (see discussion in [21,

22]). If a mutant mtDNA variant (mitotype) consti-

tutes a significant fraction of all molecules, the puri-

fying selection may occur at the whole-cell level. The

selection is enabled because, during the development

of follicular cells, the mtDNA diversity within indi-

vidual cells decreases due to the genetic bottleneck

effect (see review [23]), linking the mtDNA genotype

to the phenotype of the entire cell. At the same time,

both purifying selection against deleterious mtDNAs

with low allele frequencies and any kind of positive

selection are most likely restricted to the intracellular

level.

Selfish mtDNA is one of the challenges in the

mitochondrial replacement therapy. Mitochondrial

heteroplasmy is associated with a large number of

human hereditary diseases. Such diseases can be

transmitted from a mother to child, and their her-

itability depends on the ratio of mutant (pathogen-

ic) and normal mtDNA variants in the oocytes [24].

To prevent the spread of such diseases, scientists

have been actively developing the methods for mi-

tochondrial replacement therapy, leading to the first

live birth of a “three-parent” baby whose nuclear

DNA originated from the parents, while mtDNA was

from a donor (“third parent”) [25]. The transfer of

the spindle from the cytoplasm of the mother’s cell,

who carried the pathogenic variant of mtDNA, into

the cytoplasm of the donor cell resulted in the do-

nor’s mtDNA constituting over 99% mtDNA in the de-

veloping embryo. However, in some cases, embryonic

stem cell lines derived by this method demonstrated

a gradual increase in the pathogenic variant of the

mother’s mtDNA and loss of “healthy” donor’s mtDNA

[26], suggesting that the mutant mtDNA variant asso-

ciated with the disease had a higher intracellular fit-

ness compared to the donor mtDNA.

Examples of selfish mtDNA can be found among

invertebrates. For instance, in Caenorhabditis brigg-

sae, an mtDNA variant with a large deletion might

have an advantage in the cell, but was harmful at

the organismal level [27]. In Caenorhabditis elegans,

mtDNA variants with a large deletion have been

maintained in the state of heteroplasmy with the

wild-type mtDNA due to the effects of multidirectional

intra- and interorganismal selection. [28]. Remarkably,

mtDNA from one species can displace native mtDNA

in another species, as has been demonstrated in het-

eroplasmic fruit flies harboring two different mtDNAs

from two closely related species, Drosophila mauriti-

ana and Drosophila melanogaster [29].

Finally, an example of an organism in which self-

ish mtDNA variants can arise as a result of mutations

is baker’s yeast Saccharomyces cerevisiae. Yeast cells

inherit mtDNA from both parents (mating haploid

cells) [30]. If these parental haploid cells have dif-

ferent mitotypes, the progeny will have mitochondri-

al heteroplasmy. At the same time, some variants of

yeast mtDNA with extensive deletions (rho

−

) demon-

strated a bias in the mtDNA inheritance: crossing rho

−

cells with wild-type rho

cells led to the formation

of almost exclusively rho

−

diploid cells [31-33]. We

have recently shown that this bias can be explained

by both an increased number of mtDNA copies in

rho

−

cells and elevated intracellular fitness of rho

−

mtDNA variants compared to wild-type rho

mtDNA

variants [34]. Mutant mtDNA variants also emerged

and rapidly become fixed (remained the only vari-

ants) in yeast cells grown in the absence of selection

pressure at the whole-cell level, indicating the exis-

tence of intracellular selection favoring proliferation

of mtDNA variants with extensive deletions [35].

HYPOTHETICAL MECHANISMS

PROVIDING AN ADVANTAGE

TO SELFISH mtDNA IN THE CELL

While the presence of selfish mtDNAs in multi-

ple cell types and species has been experimentally

confirmed, the mechanisms that confer their compet-

itive advantage over wild-type DNA remain poorly

understood. Nonetheless, there are several hypothe-

ses, with a varying degree of indirect experimental

support, that aim to explain the differences in the in-

tracellular fitness between the wild-type and mutant

mtDNA mitotypes.

Increased replication initiation frequency. The

mechanism allowing one mtDNA variant to displace

another mtDNA variant may involve the differences in

the replication initiation frequency. This mechanism

implies that mutations in the mtDNA replication ori-

gin may result in the increased replication frequency

for one mtDNA variant compared to another (Fig.  2a).

Even a slight increase in the replication frequency, if

it occurs over many replication rounds, could lead to

the displacement of one mtDNA variant by another

during either individual development or across the

generations. In support of this assumption, it has

been found that the drivers for the age-associated

MURAVYOV, KNORRE1922

BIOCHEMISTRY (Moscow) Vol. 90 No. 12 2025

accumulation of mutant mtDNA are mtDNA variants

with mutations in the non-coding region containing

the OriH sequence responsible for the initiation of

mtDNA replication [16]. In D.  melanogaster fruit flies

with artificially created heteroplasmy, the “winning”

mtDNA variant was determined, at least in some cas-

es, by the sequence of the non-coding region [29].

However, the possibility of emergence of mtDNA

variants with “more active” replication origins leaves

open the question of why such variants had not ap-

peared and been fixed during the evolution. We sug-

gested that mutations increasing mtDNA fitness at

the intracellular level inevitably reduce the fitness

of these variants at the cellular or organismal lev-

els. For instance, an increased replication frequency

could reduce the transcription rate, since initiation

of one process delays the other [36]. Excessive repli-

cation initiation may increase the amount of mtDNA

per cell beyond the optimal levels, potentially causing

detrimental effects.

Advantages in the replication rate of mtDNA

molecules with large deletions. Another hypothet-

ically possible mechanism allowing some mtDNA

variants to have a higher intracellular fitness is the

difference in the duplication rate, as large deletions

reduce the time required for complete mtDNA rep-

lication (Fig. 2b). However, the key factor in this

case is the relation between the mtDNA duplication

time and replication initiation frequency, which de-

termines the proportion of replicating mtDNA mole-

cules at a given moment of time. If the fraction of

simultaneously replicating molecules is small, then

the time required for the replication of the entire

molecule should not have a significant effect on their

intracellular fitness. To illustrate this, let us consider

an extreme case, when there is only one functional

replisome in the mitochondria and the replication of

the next molecule does start until the replication of

the previous molecule is complete. Obviously, in this

case, the replication time will have no effect on the

relative intracellular fitness of the mtDNA molecules.

The elongation rate of human mitochondrial

DNA polymerase is 180-270 bases per minute [37,

38], suggesting that the replication of entire human

mtDNA molecule takes no more than 2.5 h. This is

expected to be true even considering that individual

Fig. 2. Hypothetical mechanisms allowing a particular variant of mtDNA to have a higher intracellular fitness despite the

presence of harmful mutations (see the text for discussion).

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BIOCHEMISTRY (Moscow) Vol. 90 No. 12 2025

mtDNA strands replicate asynchronously (see reviews

[39, 40]). At the same time, the half-life of mtDNA in

post-mitotic mammalian tissues is 1 to 3 weeks [41].

According to the results of computer modelling (tak-

ing into account several additional assumptions on

the mtDNA copy number in a cell), the time required

for the complete displacement of normal mtDNA by

deletion-carrying mtDNA molecules would be decades

[41]. Hence, it is unlikely that this mechanism has

a significant effect on the spread of mutant mtDNA

variants with deletions in postmitotic human tissues.

On the other hand, if mitochondrial biogenesis

and associated proliferation of mtDNA proceed rap-

idly, mutant deletion-carrying mtDNA variants might

gain an advantage. For example, when the content

of mtDNA was reduced by treatment with the DNA

intercalating agent ethidium bromide and then ethid-

ium bromide was removed, mtDNA variants with

large deletions repopulated the cells faster than the

full-length mtDNA molecules [42]. Following this line

of reasoning, mtDNA variants with deletions would

also gain an advantage in the case of elevated mtDNA

turnover, i.e., when the rates of mtDNA replication

and degradation increase simultaneously. Indeed,

mtDNA is actively degraded as a result of mitoph-

agy activation or mtDNA damage [3,  43]. Moreover,

mtDNA variants with deletions may gain a greater

relative advantage in species with a large mitochon-

drial genome and short cell cycle, which implies a

high proportion of replicating mtDNA molecules at

any given time. Such organisms include yeast species,

some of which have mitochondrial genomes exceed-

ing 100 kb [44].

Avoidance of mtDNA degradation. mtDNA is

constantly synthesized and degraded, even in postmi-

totic tissues [41]. mtDNA is also actively degraded in

germline cells, ensuring the mtDNA inheritance strict-

ly along the maternal line [45]. mtDNA degradation

occurs predominantly in the mitochondrial matrix

due to the activity of mitochondrial nucleases [46]

or during autophagy, along with the degradation of

mitochondria [47]. Theoretically, both these processes

can be selective towards some mtDNA variants com-

pared to others (Fig. 2, c, d). Let us consider these

processes separately.

Selective autophagy of mitochondria (mitophagy)

can ensuring the quality control of mtDNA, but this

requires specific mtDNA molecules to be “linked” to

protein variants encoded in these molecules [48,  49].

Such linkage is possible due to restrictions on the dif-

fusion of mtDNA-encoded complexes through the mi-

tochondrial network [50] or when the mitochondrial

dynamics processes (continuous mitochondrial fusion

and fission) are limited. For example, in Drosophi-

la, mutant mtDNA variants with harmful mutations

are eliminated via mitophagy during oogenesis [51].

This process is preceded by a decrease in the amount

of mitofusin protein responsible for the mitochon-

drial fusion, leading to the fragmentation of mito-

chondrial reticulum. It is important to note that this

mechanism takes place only in germline cells, but not

in somatic ones [51]. Therefore, selective mitophagy

in the absence of mitochondrial dynamics can lead

to the elimination of mutant mtDNA variants, thus

preventing their proliferation.

At present, no mechanism has been identified by

which selfish mtDNA could evade the control by mito-

phagy and gain advantage over the wild-type mtDNA.

However, it could be assumed that if an mtDNA vari-

ant encodes a factor that inhibits mitophagy or pro-

motes mitochondrial fusion, it can increase its own

intracellular fitness by evading the quality control

at the level of individual organelles (Fig.  2d). Despite

that mtDNA typically encodes a strictly defined set

of genes, mtDNA of some invertebrate species con-

tains ORFans – open reading frames that encode pro-

teins with no homology to any known protein, but

subjected to the purifying selection pressure [52,  53].

Although the functions of the encoded proteins re-

main unknown, we propose that they might modulate

the mitophagy or mitochondrial dynamics, thereby

contributing to the increased intracellular fitness of

mtDNA variants harboring them.

Another mechanism of mtDNA degradation is as-

sociated with the activity of nucleases located in the

mitochondrial matrix. The presence of double-strand

breaks in mtDNA triggers rapid degradation of lin-

ear mtDNA fragments, driven by the exonuclease

activities of mtDNA polymerase gamma and MGME1

nuclease [54]. A deficit in the exonuclease activity

can drive accumulation of deletion-carrying mtDNA

variants, as was found in mice with a homozygous

mutation in the mitochondrial mtDNA polymerase

gene (PolG

D257A/D257A

), leading to the disruption of its

exonuclease activity [55]. The degradation of male

mtDNA in Drosophila spermatids requires the presence

of another mitochondrial endonuclease, EndoG [56],

and exonuclease Poldip2 [46]. Finally, the mitochon-

drial genomes of some fungal species contain hom-

ing endonucleases capable of cleaving DNA and then

integrating their coding sequence at the site of the

double-strand break. This allows endonuclease genes

to spread in the population as a selfish element of

mitochondrial genome [57, 58]. Taken together, these

data suggest that mtDNA variants whose sequences

lack the sites for hydrolysis with mitochondrial nucle-

ases may gain an advantage under conditions when

mtDNA is actively degraded (Fig. 2c), e.g., as a result

of damage or during certain life cycle stages.

Survival of the weakest. In 1996, Aubrey de Grey

proposed that the wild-type mtDNA associated with

a fully functional respiratory chain might be more

MURAVYOV, KNORRE1924

BIOCHEMISTRY (Moscow) Vol. 90 No. 12 2025

susceptible to degradation than mutant mtDNA un-

able to provide an assembly of the functional respi-

ratory chain [59]. This hypothesis was named “sur-

vival of the weakest” (Fig.2e). Indeed, in some cases,

mitochondrial respiratory chain can be a source of

reactive oxygen species (ROS) [60, 61] that cause mu-

tations in mtDNA. This is consistent with the fact

that the C to T mutations typical of oxidative damage

in a single-stranded DNA, dominate in vertebrates

[62, 63]. At the same time, the damage to mtDNA

caused by hydrogen peroxide (one of ROS forms) can

induce mtDNA degradation [64].

However, it should be noted that this hypothe-

sis has not been confirmed experimentally, likely be-

cause there are other factors that can exert a strong

effect in the opposite direction. Indeed, the import

of mitochondrial proteins essential for mtDNA rep-

lication depends on the transmembrane potential at

the inner mitochondrial membrane and ATP content

in the mitochondrial matrix [65]. Therefore, mutant

variants unable to provide formation of the func-

tional respiratory chain and ATP synthase will be at

a disadvantage in this respect. Moreover, mitochon-

dria in cells actively fuse and divide, which equaliz-

es their content throughout the cell’s mitochondrial

network [66, 67] and makes it difficult to link spe-

cific mtDNA molecules to the areas of mitochondria

enriched with proteins encoded in them.

CONCLUSION

mtDNA selection occurs simultaneously at sever-

al organizational levels. Consequently, the emergence

of selfish mtDNA variants that have a replicative ad-

vantage but are detrimental to the cell or multicel-

lular organism is possible. Despite the mechanisms

that eliminate mutant mtDNA, selfish mtDNAs can

emerge in nature and experimental systems, that

might have an advantage due to a faster replication

or ability to evade degradation. Therefore, eukaryotic

organisms are under continuous pressure created by

the potential emergence of such mtDNA.

We propose that during the early stages of eu-

karyotic evolution, before the mitochondrial quali-

ty control systems evolved to suppress proliferation

of mutant mtDNA, selfish mtDNAs had posed a sig-

nificant challenge to eukaryotic cells. This pressure

has likely drove the evolution of cellular mecha-

nisms protecting against selfish mtDNA. Such mech-

anisms may include control of mtDNA copy number

in the germlines of multicellular animals [68], se-

lective mitophagy [69], and uniparental inheritance

of mtDNA in most eukaryotic species [70], which

prevents the horizontal transfer of selfish mtDNA

within populations.

Abbreviations

mtDNA mitochondrial DNA

Acknowledgments

This work is dedicated to the anniversary of Vladimir

Petrovich Skulachev, whose inexhaustible scientific

enthusiasm and original ideas have inspired the au-

thors of this review. We are grateful to Boris Alexan-

drovich Feniouk for discussing our work and provid-

ing critical comments.

Contributions

G.M. and D.K. analyzed the published articles and

wrote the manuscript; D.K. prepared the figures.

Funding

This work (all sections except “Avoidance of mtDNA

degradation”) was supported by the Russian Science

Foundation (project no.22-14-00108-П); “Avoidance of

mtDNA degradation” section was written as a part of

the State Assignment to the Lomonosov Moscow State

University (project no.AAAA-A19-119031390114-5).

Ethics approval and consent to participate

This work does not contain any studies involving

human or animal subjects.

Conflict of interest

The authors of this work declare that they have

noconflicts of interest.

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REFERENCES

1. Roger, A. J., Muñoz-Gómez, S. A., and Kamikawa, R.

(2017) The origin and diversification of mitochondria,

Curr. Biol., 27, R1177-R1192, https://doi.org/10.1016/

j.cub.2017.09.015.

MECHANISMS OF INTRACELLULAR SELECTION OF MITOCHONDRIAL DNA 1925

BIOCHEMISTRY (Moscow) Vol. 90 No. 12 2025

2. Taanman, J. W. (1999) The mitochondrial genome:

structure, transcription, translation and replica-

tion, Biochim. Biophys. Acta, 1410, 103-123, https://

doi.org/10.1016/s0005-2728(98)00161-3.

3. Medeiros, T. C., Thomas, R. L., Ghillebert, R., and

Graef, M. (2018) Autophagy balances mtDNA syn-

thesis and degradation by DNA polymerase POLG

during starvation, J. Cell Biol., 217, 1601-1611, https://

doi.org/10.1083/jcb.201801168.

4. Zhang, Q., Wang, Z., Zhang, W., Wen, Q., Li, X.,

Zhou,J., Wu,X., Guo,Y., Liu,Y., Wei,C., Qian,W., and

Tian,Y. (2021) The memory of neuronal mitochondri-

al stress is inherited transgenerationally via elevated

mitochondrial DNA levels, Nat. Cell Biol., 23, 870-880,

https://doi.org/10.1038/s41556-021-00724-8.

5. Galeota-Sprung, B., Fernandez,A., and Sniegowski,P.

(2022) Changes to the mtDNA copy number during

yeast culture growth, R. Soc. Open Sci., 9, 211842,

https://doi.org/10.1098/rsos.211842.

6. De Giorgi, C., and Saccone, C. (1989) Mitochondri-

al genome in animal cells. Structure, organiza-

tion, and evolution, Cell Biophys., 14, 67-78, https://

doi.org/10.1007/BF02797392.

7. Rand, D.M. (2001) The units of selection on mitochon-

drial DNA, Annu Rev Ecol Syst, 32, 415-448, https://

doi.org/10.1146/annurev.ecolsys.32.081501.114109.

8. Rossignol, R., Faustin, B., Rocher, C., Malgat, M.,

Mazat, J.-P., and Letellier, T. (2003) Mitochondrial

threshold effects, Biochem. J., 370, 751-762, https://

doi.org/10.1042/BJ20021594.

9. Wallace, D.C. (1986) Mitotic segregation of mitochon-

drial DNAs in human cell hybrids and expression of

chloramphenicol resistance, Somat. Cell Mol. Genet.,

12, 41-49, https://doi.org/10.1007/BF01560726.

10. Greaves, L. C., Preston, S. L., Tadrous, P. J., Taylor,

R. W., Barron, M. J., Oukrif, D., Leedham, S. J.,

Deheragoda,M., Sasieni,P., Novelli, M.R., Jankowski,

J.A.Z., Turnbull, D.M., Wright, N.A., and McDonald,

S. A. C. (2006) Mitochondrial DNA mutations are

established in human colonic stem cells, and mu-

tated clones expand by crypt fission, Proc. Natl.

Acad. Sci. USA, 103, 714-719, https://doi.org/10.1073/

pnas.0505903103.

11. Ågren, J. A., and Clark, A. G. (2018) Selfish genet-

ic elements, PLoS Genet., 14, e1007700, https://

doi.org/10.1371/journal.pgen.1007700.

12. Khrapko, K., Bodyak, N., Thilly, W. G., van Orsouw,

N. J., Zhang, X., Coller, H. A., Perls, T. T., Upton, M.,

Vijg, J., and Wei, J. Y. (1999) Cell-by-cell scanning

of whole mitochondrial genomes in aged human

heart reveals a significant fraction of myocytes with

clonally expanded deletions, Nucleic Acids Res., 27,

2434-2441, https://doi.org/10.1093/nar/27.11.2434.

13. Taylor, S.D., Ericson, N.G., Burton, J.N., Prolla, T.A.,

Silber, J. R., Shendure, J., and Bielas, J. H. (2014)

Targeted enrichment and high-resolution digital

profiling of mitochondrial DNA deletions in human

brain, Aging Cell, 13, 29-38, https://doi.org/10.1111/

acel.12146.

14. Nekhaeva,E., Bodyak, N.D., Kraytsberg,Y., McGrath,

S. B., Van Orsouw, N. J., Pluzhnikov, A., Wei, J. Y.,

Vijg, J., and Khrapko, K. (2002) Clonally expanded

mtDNA point mutations are abundant in individual

cells of human tissues, Proc. Natl. Acad. Sci. USA, 99,

5521-5526, https://doi.org/10.1073/pnas.072670199.

15. Jenuth, J. P., Peterson, A. C., and Shoubridge, E. A.

(1997) Tissue-specific selection for different mtDNA

genotypes in heteroplasmic mice, Nat. Genet., 16,

93-95, https://doi.org/10.1038/ng0597-93.

16. Korotkevich, E., Conrad, D. N., Gartner, Z. J., and

O’Farrell, P. H. (2025) Selfish mutations promote

age-associated erosion of mtDNA integrity in mam-

mals, Nat. Commun., 16, 5435, https://doi.org/10.1038/

s41467-025-60477-y.

17. Stewart, J. B., Freyer, C., Elson, J. L., Wredenberg, A.,

Cansu, Z., Trifunovic, A., and Larsson, N.-G. (2008)

Strong purifying selection in transmission of mam-

malian mitochondrial DNA, PLoS Biol., 6, e10, https://

doi.org/10.1371/journal.pbio.0060010.

18. Wei, W., Tuna, S., Keogh, M. J., Smith, K. R., Aitman,

T. J., Beales, P. L., Bennett, D. L., Gale, D. P., Bitner-

Glindzicz, M.A.K., Black, G.C., Brennan,P., Elliott,P.,

Flinter, F. A., Floto, R. A., Houlden, H., Irving, M.,

Koziell, A., Maher, E. R., Markus, H. S., et al. (2019)

Germline selection shapes human mitochondri-

al DNA diversity, Science, 364, eaau6520, https://

doi.org/10.1126/science.aau6520.

19. Franco,M., Pickett, S.J., Fleischmann,Z., Khrapko,M.,

Cote-L’Heureux,A., Aidlen,D., Stein,D., Markuzon,N.,

Popadin, K., Braverman, M., Woods, D. C., Tilly, J. L.,

Turnbull, D. M., and Khrapko, K. (2022) Dynamics

of the most common pathogenic mtDNA variant

m.3243A > G demonstrate frequency-dependen-

cy in blood and positive selection in the germline,

Hum. Mol. Genet., 31, 4075-4086, https://doi.org/

10.1093/hmg/ddac149.

20. Zhang, H., Esposito, M., Pezet, M. G., Aryaman, J.,

Wei,W., Klimm,F., Calabrese,C., Burr, S.P., Macabelli,

C. H., Viscomi, C., Saitou, M., Chiaratti, M. R., Stew-

art, J. B., Jones, N., and Chinnery, P. F. (2021) Mito-

chondrial DNA heteroplasmy is modulated during

oocyte development propagating mutation transmis-

sion, Sci. Adv., 7, eabi5657, https://doi.org/10.1126/

sciadv.abi5657.

21. Franco, M., Cote-L’Heureux, A., Fleischmann, Z.,

Chen, Z., Khrapko, M., Vyshedskiy, B., Braver-

man, M., Popadin, K., Pickett, S., Woods, D. C., Tilly,

J. L., Turnbull, D., and Khrapko, K. (2023) A nov-

el, wave-shaped profile of germline selection of

pathogenic mtDNA mutations is discovered by by-

passing a classical statistical bias, bioRxiv, https://

doi.org/10.1101/2023.11.21.568140.

MURAVYOV, KNORRE1926

BIOCHEMISTRY (Moscow) Vol. 90 No. 12 2025

22. Fleischmann, Z., Cote-L’Heureux, A., Franco, M.,

Oreshkov, S., Annis, S., Khrapko, M., Aidlen, D.,

Popadin,K., Woods, D.C., Tilly, J.L., and Khrapko,K.

(2024) Reanalysis of mtDNA mutations of human

primordial germ cells (PGCs) reveals NUMT con-

tamination and suggests that selection in PGCs

may be positive, Mitochondrion, 74, 101817, https://

doi.org/10.1016/j.mito.2023.10.005.

23. Mishra, P., and Chan, D. C. (2014) Mitochondrial dy-

namics and inheritance during cell division, devel-

opment and disease, Nat. Rev. Mol. Cell Biol., 15,

634-646, https://doi.org/10.1038/nrm3877.

24. Taylor, R.W., and Turnbull, D.M. (2005) Mitochondri-

al DNA mutations in human disease, Nat. Rev. Genet.,

6, 389-402, https://doi.org/10.1038/nrg1606.

25. Zhang, J., Liu, H., Luo, S., Chavez-Badiola, A., Liu, Z.,

Yang, M., Munne, S., Konstantinidis, M., Wells, D.,

and Huang, T. (2016) First live birth using human

oocytes reconstituted by spindle nuclear transfer

for mitochondrial DNA mutation causing Leigh syn-

drome, Fertil. Steril., 106, e375-e376, https://doi.org/

10.1016/j.fertnstert.2016.08.004.

26. Kang, E., Wu, J., Gutierrez, N. M., Koski,A., Tippner-

Hedges,R., Agaronyan,K., Platero-Luengo,A., Martinez-

Redondo,P., Ma,H., Lee,Y., Hayama,T., van Dyken,C.,

Wang, X., Luo, S., Ahmed, R., Li, Y., Ji, D., Kayali, R.,

Cinnioglu,C., etal. (2016) Mitochondrial replacement

in human oocytes carrying pathogenic mitochon-

drial DNA mutations, Nature, 540, 270-275, https://

doi.org/10.1038/nature20592.

27. Clark, K. A., Howe, D. K., Gafner, K., Kusuma, D.,

Ping,S., Estes, S., and Denver, D.R. (2012) Selfish lit-

tle circles: transmission bias and evolution of large

deletion-bearing mitochondrial DNA in Caenorhabdi-

tis briggsae nematodes, PLoS One, 7, e41433, https://

doi.org/10.1371/journal.pone.0041433.

28. Gitschlag, B.L., Pereira, C.V., Held, J. P., McCandlish,

D. M., and Patel, M. R. (2024) Multiple distinct evo-

lutionary mechanisms govern the dynamics of self-

ish mitochondrial genomes in Caenorhabditis ele-

gans, Nat. Commun., 15, 8237, https://doi.org/10.1038/

s41467-024-52596-9.

29. Ma, H., and O’Farrell, P. H. (2016) Selfish drive can

trump function when animal mitochondrial genomes

compete, Nat. Genet., 48, 798-802, https://doi.org/

10.1038/ng.3587.

30. Linnane, A. W., Saunders, G. W., Gingold, E. B., and

Lukins, H. B. (1968) The biogenesis of mitochondria.

V. Cytoplasmic inheritance of erythromycin resistance

in Saccharomyces cerevisiae, Proc. Natl. Acad. Sci.

USA, 59, 903-910, https://doi.org/10.1073/pnas.59.3.903.

31. Ephrussi, B., de Margerie-Hottinguer, H., and

Roman, H. (1955) Suppressiveness: a new factor in

the genetic determinism of the synthesis of respira-

tory enzymes in yeast, Proc. Natl. Acad. Sci. USA, 41,

1065-1071, https://doi.org/10.1073/pnas.41.12.1065.

32. De Zamaroczy, M., Marotta, R., Faugeron-Fonty, G.,

Goursot,R., Mangin,M., Baldacci,G., and Bernardi,G.

(1981) The origins of replication of the yeast mito-

chondrial genome and the phenomenon of suppres-

sivity, Nature, 292, 75-78, https://doi.org/10.1038/

292075a0.

33. Karavaeva, I. E., Golyshev, S. A., Smirnova, E. A.,

Sokolov, S. S., Severin, F. F., and Knorre, D. A. (2017)

Mitochondrial depolarization in yeast zygotes inhib-

its clonal expansion of selfish mtDNA, J. Cell Sci., 130,

1274-1284, https://doi.org/10.1242/jcs.197269.

34. Kashko, N.D., Muravyov,G., Karavaeva,I., Glagoleva,

E. S., Logacheva, M. D., Garushyants, S. K., and

Knorre, D.A. (2025) Inheritance bias of deletion-har-

bouring mtDNA in yeast: The role of copy number

and intracellular selection, PLoS Genet., 21, e1011737,

https://doi.org/10.1371/journal.pgen.1011737.

35. Taylor, D.R., Zeyl,C., and Cooke,E. (2002) Conflicting

levels of selection in the accumulation of mitochon-

drial defects in Saccharomyces cerevisiae, Proc. Natl.

Acad. Sci. USA, 99, 3690-3694, https://doi.org/10.1073/

pnas.072660299.

36. Røyrvik, E. C., and Johnston, I. G. (2020) MtDNA se-

quence features associated with “selfish genomes”

predict tissue-specific segregation and reversion,

Nucleic Acids Res., 48, 8290-8301, https://doi.org/

10.1093/nar/gkaa622.

37. Clayton, D.A. (1982) Replication of animal mitochon-

drial DNA, Cell, 28, 693-705, https://doi.org/10.1016/

0092-8674(82)90049-6.

38. Korhonen, J. A., Pham, X. H., Pellegrini, M., and

Falkenberg, M. (2004) Reconstitution of a minimal

mtDNA replisome in vitro, EMBO J., 23, 2423-2429,

https://doi.org/10.1038/sj.emboj.7600257.

39. Yasukawa, T., and Kang, D. (2018) An overview of

mammalian mitochondrial DNA replication mech-

anisms, J. Biochem., 164, 183-193, https://doi.org/

10.1093/jb/mvy058.

40. Falkenberg, M., and Gustafsson, C. M. (2020) Mam-

malian mitochondrial DNA replication and mecha-

nisms of deletion formation, Crit. Rev. Biochem. Mol.

Biol., 55, 509-524, https://doi.org/10.1080/10409238.

2020.1818684.

41. Kowald,A., Dawson,M., and Kirkwood, T.B.L. (2014)

Mitochondrial mutations and ageing: can mitochon-

drial deletion mutants accumulate via a size based

replication advantage? J. Theor. Biol., 340, 111-118,

https://doi.org/10.1016/j.jtbi.2013.09.009.

42. Diaz, F., Bayona-Bafaluy, M. P., Rana, M., Mora, M.,

Hao, H., and Moraes, C. T. (2002) Human mitochon-

drial DNA with large deletions repopulates organelles

faster than full-length genomes under relaxed copy

number control, Nucleic Acids Res., 30, 4626-4633,

https://doi.org/10.1093/nar/gkf602.

43. Seshadri, A., and Badrinarayanan, A. (2025) Exonu-

clease action of replicative polymerase gamma drives

MECHANISMS OF INTRACELLULAR SELECTION OF MITOCHONDRIAL DNA 1927

BIOCHEMISTRY (Moscow) Vol. 90 No. 12 2025

damage-induced mitochondrial DNA clearance,

EMBO Rep., 26, 1385-1405, https://doi.org/10.1038/

s44319-025-00380-1.

44. Freel, K. C., Friedrich, A., and Schacherer, J. (2015)

Mitochondrial genome evolution in yeasts: an all-

encompassing view, FEMS Yeast Res., 15, fov023,

https://doi.org/10.1093/femsyr/fov023.

45. Sato, M., and Sato, K. (2013) Maternal inheritance

of mitochondrial DNA by diverse mechanisms to

eliminate paternal mitochondrial DNA, Biochim. Bio-

phys. Acta, 1833, 1979-1984, https://doi.org/10.1016/

j.bbamcr.2013.03.010.

46. Chen, Z., Zhang, F., Lee, A., Yamine, M., Wang, Z.-H.,

Zhang, G., Combs, C., and Xu, H. (2025) Mitochon-

drial DNA removal is essential for sperm develop-

ment and activity, EMBO J., 44, 1749-1773, https://

doi.org/10.1038/s44318-025-00377-5.

47. Lim, Y., Rubio-Peña, K., Sobraske, P. J., Molina,

P. A., Brookes, P. S., Galy, V., and Nehrke, K. (2019)

Fndc-1 contributes to paternal mitochondria elim-

ination in C. elegans, Dev. Biol., 454, 15-20, https://

doi.org/10.1016/j.ydbio.2019.06.016.

48. Busch, K. B., Kowald, A., and Spelbrink, J. N. (2014)

Quality matters: how does mitochondrial network

dynamics and quality control impact on mtDNA in-

tegrity? Philos. Trans. R. Soc. Lond. B Biol. Sci., 369,

20130442, https://doi.org/10.1098/rstb.2013.0442.

49. Knorre, D. A. (2020) Intracellular quality control of

mitochondrial DNA: evidence and limitations, Phi-

los. Trans. R. Soc. Lond. B Biol. Sci., 375, 20190176,

https://doi.org/10.1098/rstb.2019.0176.

50. Wilkens, V., Kohl, W., and Busch, K. (2013) Restrict-

ed diffusion of OXPHOS complexes in dynamic mi-

tochondria delays their exchange between cristae

and engenders a transitory mosaic distribution,

J. Cell Sci., 126, 103-116, https://doi.org/10.1242/

jcs.108852.

51. Lieber,T., Jeedigunta, S.P., Palozzi, J.M., Lehmann,R.,

and Hurd, T. R. (2019) Mitochondrial fragmentation

drives selective removal of deleterious mtDNA in

the germline, Nature, 570, 380-384, https://doi.org/

10.1038/s41586-019-1213-4.

52. Milani,L., Ghiselli,F., Maurizii, M.G., Nuzhdin, S.V.,

and Passamonti, M. (2014) Paternally transmitted

mitochondria express a new gene of potential vi-

ral origin, Genome Biol. Evol., 6, 391-405, https://

doi.org/10.1093/gbe/evu021.

53. Selifanova, M., Demianchenko, O., Noskova, E.,

Pitikov, E., Skvortsov, D., Drozd, J., Vatolkina, N.,

Apel, P., Kolodyazhnaya, E., Ezhova, M. A., Tzetlin,

A.B., Neretina, T.V., and Knorre, D.A. (2023) ORFans

in mitochondrial genomes of marine polychaete Poly-

dora, Genome Biol. Evol., 15, evad219, https://doi.org/

10.1093/gbe/evad219.

54. Peeva, V., Blei, D., Trombly, G., Corsi, S., Szukszto,

M. J., Rebelo-Guiomar, P., Gammage, P. A., Kudin,

A.P., Becker,C., Altmüller,J., Minczuk,M., Zsurka,G.,

and Kunz, W. S. (2018) Linear mitochondrial DNA

is rapidly degraded by components of the repli-

cation machinery, Nat. Commun., 9, 1727, https://

doi.org/10.1038/s41467-018-04131-w.

55. Nissanka,N., Bacman, S.R., Plastini, M.J., and Moraes,

C. T. (2018) The mitochondrial DNA polymerase

gamma degrades linear DNA fragments precluding

the formation of deletions, Nat. Commun., 9, 2491,

https://doi.org/10.1038/s41467-018-04895-1.

56. DeLuca, S. Z., and O’Farrell, P. H. (2012) Barri-

ers to male transmission of mitochondrial DNA in

sperm development, Dev. Cell, 22, 660-668, https://

doi.org/10.1016/j.devcel.2011.12.021.

57. Wolters, J.F., LaBella, A.L., Opulente, D.A., Rokas,A.,

and Hittinger, C. T. (2023) Mitochondrial genome di-

versity across the subphylum Saccharomycotina,

Front. Microbiol., 14, 1268944, https://doi.org/10.3389/

fmicb.2023.1268944.

58. Megarioti, A. H., and Kouvelis, V. N. (2020) The co-

evolution of fungal mitochondrial introns and their

homing endonucleases (GIY-YIG and LAGLIDADG),

Genome Biol. Evol., 12, 1337-1354, https://doi.org/

10.1093/gbe/evaa126.

59. De Grey, A. D. (1997) A proposed refinement of the

mitochondrial free radical theory of aging, Bioessays,

19, 161-166, https://doi.org/10.1002/bies.950190211.

60. Chernyak, B. V., Izyumov, D. S., Lyamzaev, K. G.,

Pashkovskaya, A. A., Pletjushkina, O. Y., Antonenko,

Y.N., Sakharov, D.V., Wirtz, K. W.A., and Skulachev,

V. P. (2006) Production of reactive oxygen spe-

cies in mitochondria of HeLa cells under oxida-

tive stress, Biochim. Biophys. Acta, 1757, 525-534,

https://doi.org/10.1016/j.bbabio.2006.02.019.

61. Skulachev, V. P. (2002) Programmed death phenome-

na: from organelle to organism, Ann. NY Acad. Sci.,

959, 214-237, https://doi.org/10.1111/j.1749-6632.2002.

tb02095.x.

62. Degtyareva, N. P., Saini, N., Sterling, J. F., Placentra,

V. C., Klimczak, L. J., Gordenin, D. A., and Doetsch,

P. W. (2019) Mutational signatures of redox stress

in yeast single-strand DNA and of aging in human

mitochondrial DNA share a common feature, PLoS

Biol., 17, e3000263, https://doi.org/10.1371/journal.

pbio.3000263.

63. Iliushchenko, D., Efimenko, B., Mikhailova, A. G.,

Shamanskiy, V., Saparbaev, M. K., Matkarimov, B. T.,

Mazunin, I., Voronka, A., Knorre, D., Kunz, W. S.,

Kapranov, P., Denisov, S., Fellay, J., Khrapko, K.,

Gunbin, K., and Popadin, K. (2025) Deciphering the

foundations of mitochondrial mutational spectra:

replication-driven and damage-induced signatures

across chordate classes, Mol. Biol. Evol., 42, msae261,

https://doi.org/10.1093/molbev/msae261.

64. Shokolenko, I., Venediktova, N., Bochkareva, A.,

Wilson, G. L., and Alexeyev, M. F. (2009) Oxidative

MURAVYOV, KNORRE1928

BIOCHEMISTRY (Moscow) Vol. 90 No. 12 2025

stress induces degradation of mitochondrial DNA,

Nucleic Acids Res., 37, 2539-2548, https://doi.org/

10.1093/nar/gkp100.

65. Wiedemann, N., and Pfanner, N. (2017) Mitochon-

drial machineries for protein import and assembly,

Annu. Rev. Biochem., 86, 685-714, https://doi.org/

10.1146/annurev-biochem-060815-014352.

66. Quintana-Cabrera, R., and Scorrano, L. (2023) Deter-

minants and outcomes of mitochondrial dynamics,

Mol. Cell, 83, 857-876, https://doi.org/10.1016/j.molcel.

2023.02.012.

67. Yang, L., Long, Q., Liu, J., Tang, H., Li, Y., Bao, F.,

Qin, D., Pei, D., and Liu, X. (2015) Mitochondrial fu-

sion provides an “initial metabolic complementation”

controlled by mtDNA, Cell. Mol. Life Sci., 72, 2585-

2598, https://doi.org/10.1007/s00018-015-1863-9.

68. Edwards, D. M., Røyrvik, E. C., Chustecki, J. M.,

Giannakis,K., Glastad, R.C., Radzvilavicius, A.L., and

Johnston, I. G. (2021) Avoiding organelle mutational

meltdown across eukaryotes with or without a

germline bottleneck, PLoS Biol., 19, e3001153,

https://doi.org/10.1371/journal.pbio.3001153.

69. Palozzi, J. M., Jeedigunta, S. P., Minenkova, A. V.,

Monteiro, V.L., Thompson, Z.S., Lieber,T., and Hurd,

T.R. (2022) Mitochondrial DNA quality control in the

female germline requires a unique programmed

mitophagy, Cell Metab., 34, 1809-1823.e6, https://

doi.org/10.1016/j.cmet.2022.10.005.

70. Birky, C. W., Jr. (2008) Uniparental inheritance of

organelle genes, Curr. Biol., 18, R692-R695, https://

doi.org/10.1016/j.cub.2008.06.049.

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