**Abstract**

 The mitochondrial genomic material (mtDNA), similarly to nuclear genome, is exposed to a plethora of exogenous and endogenous agents, as well as natural processes like replication that compromise the integrity and fidelity of the mtDNA, despite the abovementioned, the mtDNA does not contain genes involved in DNA repair, therefore mitochondria completely depend on the importation of nuclear-encoded elements to achieve genome maintenance, which implies a coordinated crosstalk between these two organelles. It has been determined that to counteract damage, mitochondria possess well-defined repair pathways quite similar to those of the nucleus, among which are: base excision repair (BER), mismatch repair (MMR), single-strand break repair (SSBR), microhomology-mediated end joining (MMEJ), and probably homology recombination dependent repair (HRR). If these repair pathways are nonfunctional and the lesions remain unrepaired, the emergence of mutations, deletions, and other insults may result in compromised cellular viability and disease.

**Keywords:** mitochondria, mtDNA, damage, repair, BER, MMR, SSBR, HRR, MMEJ

#### **1. Introduction**

The mitochondrion is an essential organelle involved principally in the production of ATP and other metabolites which are important to several cellular functions, besides this organelle participates in other processes as iron-sulfur cluster biogenesis, heme production, and calcium regulation [1]. The mitochondrion possesses its own circular genomic material (mtDNA), which is exposed to the same DNA lesions as nuclear genome is, however, unlike the latter, mtDNA does not encode for genes involved in DNA maintenance or repair which implies that these processes completely depend on nuclear-encoded elements translocated to mitochondria. It was first thought that mitochondria lacked the ability to repair its DNA material, and this assumption was originated due to the observation of the absence of pyrimidine dimer resolution after ultra violet light exposition in mammalian cells [2]; however, nowadays, the study of mtDNA repair pathways has evolved into a complete research area that is constantly growing, since it has been observed that mitochondria not only possess some of the nuclear-conserved mechanisms like: base excision repair (BER), mismatch repair (MMR), single-strand break repair (SSBR), microhomology-mediated end joining (MMEJ), and homologous recombination

dependent repair (HRR), additionally mitochondria have evolved specific unique methods to deal with mtDNA insults based on the redundancy nature of mtDNA and mitochondrion itself, if the damage surpasses its repair capabilities, the mtDNA molecules can be destroyed and replicated again or even the whole organelle can be degraded [3]. Of importance, lesions that remain unrepaired in mtDNA such as deletions, mutations, inversions, and other rearrangements have been linked to several heritable disease syndromes [4]; further, mtDNA rearrangements and deletions have been associated with aging and cancer (www.mitomap.org/org/ MITOMAP) [5]. In this chapter, we will summarize the different mechanisms by which the mammalian mtDNA can be damaged and the described pathways that are involved in maintenance of fidelity and integrity of mitochondrial genome.

## **2. The mitochondrial genome**

One of the features of mammalian cells is that they have two DNA-containing compartments: nuclei and mitochondria. Nuclear genome is large, diploid, and linear; in contrast, mitochondrial genome is polyploid and quite small, since is formed by a 16,569 pb circular molecule that accounts for 0.0005% of the human genome and 0.1% of the total number of genes in the human; mtDNA is redundant, since a few hundred to few thousand copies can be found per cell [3], when all the copies are identical, the genotype is termed homoplasmy, instead when multiple forms exist within the same tissue or cell; the genotype is called heteroplasmy [6]. The mitochondrial genome presents 37 genes, 13 of which encode for proteins oxidative phosphorylation chain specific and the remaining are implicated in translation: 2 ribosomal RNAs (small of 12S and large of 16S) and 22 tRNAs. The grade of compaction of mtDNA is interesting since it has no introns, and the intergenic regions are almost absent, additionally there are two noncoding regions: one of approximately 1 kb known as noncoding region (NCR) and another small of 30 bp, both implicated in regulation of replication and transcription [7]. The NCR presents a triple stranded region, named D-loop, which occupies most of its extension and is related to the start of transcription [8], besides it has been observed that some genes overlap and others lack termination codons; therefore, it has been established that the promoters produce polycistronic transcripts which are further processed to generate mature RNA molecules [9]. As mentioned above, some of the proteins involved in respiratory system and ATP synthesis, which are extremely important to cellular functions, are encoded by mtDNA and not the nuclear genome, thus it is important to maintain mitochondrial genome integrity to preserve homeostasis [10].

Despite the advances made in the study of mtDNA replication mechanism, the exact machinery and steps involved in this procedure are not fully known; however, it has been determined a general head core to this process which consists of the polymerase gamma (Polγ), a DNA helicase named Twinkle, and the mitochondrial single-stranded binding protein (mtSSB) [11]. Nowadays, there are three proposed models to explain mtDNA replication: (1) the first is quite similar to nucleus DNA replication, with standard leading and lagging strand replication, (2) a strand displacement model, where the lagging strand is synthetized once the leading has advanced and synthetized a long fragment, and (3) in this model, the lagging strand is hybridized with complementary RNA, a mechanism termed RNA incorporation throughout the lagging strand (RITOL) [8]. Another interesting feature about mtDNA replication is that contrary to what occurs in nuclear genome, mitochondrial genome replication is not limited to S phase of the cell cycle [12].

Unlike the nucleus, where the DNA forms part of nucleoprotein complexes, consisting of DNA molecules wrapped around histone structures, the mitochondrial

*Mitochondrial Genome Maintenance: Damage and Repair Pathways DOI: http://dx.doi.org/10.5772/intechopen.84627* 

genome does not present histones. It has been thought that this lack is responsible of the high rate of mtDNA mutagenesis, which is 10-fold greater than that in nucleus; however, this hypothesis is controversial since experimental evidence has suggested that histones might provoke DNA damage instead of preventing it [3]. Despite the above, mitochondrial genome is not naked; it is packaged into protein-DNA complexes, which are termed mitochondrial nucleoids due to its similarity to bacterial chromosomes [13]. The most abundant nucleoid-associated proteins are mtSSB, transcription factor A of mitochondria (TFAM), Polγ, mitochondrial RNA polymerase (POLRMT), and Twinkle DNA helicase [14].

## **3. Sources of mtDNA damage**

Mitochondrial genome is exposed to almost the same insults that nuclear genome is, which can be originated by internal and external sources. Six types of DNA damage have been proposed to be the more relevant in mitochondria [3].

#### **3.1 Alkylation damage**

This kind of lesion may be due to exposition to exogenous agents as chemotherapeutic drugs, diet, and tobacco smoke; however, DNA alkylation damage can also be generated from the interaction of DNA with endogenous molecules [15], such as betaine, choline, and S-adenosylmethionine (SAM); the latter is the most relevant alkylating agent in the cell; SAM is a co-substrate involved in the transfer of methyl groups, when incubated with DNA in aqueous solutions leads to base modification, forming small amounts of 7-methylguanine and 3-methyladenine nonenzymatically, therefore SAM acts as a weak DNA-alkylating agent [16]. Of interest, these DNA modifications, in specific 7-methylguanine can trigger the formation of mutagenic apurinic sites (AP) and imidazole ring opening which results in the stoppage of replication machinery [17]; moreover, 3-methylguanine itself is a cytotoxic DNA lesion that also blocks replication [15]. Interestingly, mitochondria store about 30% of total hepatic SAM [18], thus mtDNA is constantly exposed to this alkylating agent, which threats its stability and integrity.

#### **3.2 Hydrolytic damage**

There are two types of hydrolytic damage, the first is the formation of AP sites as a product of hydrolysis of the glycosidic bonds between bases and deoxyribose, and these lesions could appear due to heating, alkylation damage (previously mentioned) or by the action of N-glycosylases [19]. It has been estimated that AP is one of the most frequent lesions in the DNA, with approximately 10,000 lesions per cell, per day [20]. Interestingly, typical AP sites generate base pair modifications, since there is a preference to incorporate adenine opposite to AP by polymerases during DNA replication [21]. The other form of hydrolytic damage is the hydrolytic deamination of bases, where cytosine and its homolog 5-methylcitosine are mainly affected. It is noteworthy that the conversion of cytosine to uracil may introduce punctual mutations to the genome during replication if left unrepaired [20].

#### **3.3 Formation of adducts**

This type of lesions can be generated for exposition to ultraviolet type B and C light which produce bulky DNA adducts termed photodimers, in addition, activated metabolites of several organic contaminants, for example, polycyclic aromatic

hydrocarbons and mycotoxins may bring about adducts [1]. On the other hand, adduct formation can also be stimulated by endogenous factors, for example, it has been demonstrated that reactive intermediate products of diethylstilbestrol metabolization form DNA adducts preferentially with mitochondrial genome, where these insults are suggested to avoid replication and/or transcription, thus producing mtDNA instability in vivo [22].

## **3.4 Mismatches**

During replication, polymerases can introduce base to base mismatches as well as generate nucleotide insertions or deletions in mitochondria, which are normally known as insertion-deletion loops (IDLs). One important source of mismatches are damaged deoxyribonucleotide triphosphates (dNTPs), predominantly oxidized, which can be incorporated to DNA during synthesis [3, 10].
