*4.6.1 Sanitation of the dNTP pool*

 The DNA is not the only molecule susceptible to chemical damage, the deoxyribonucleotide triphosphates (dNTPs) pool is also affected, being oxidative damage one of the most recurrent alterations [79]. If unrepaired, these lesions could become a source of mismatch errors during DNA synthesis [3]. To cope with this threat, mitochondria have MTH1, an specialized enzyme also found in the nucleus, which can hydrolyze oxidized dNTPs such as 8-oxo-20-deoxyguanosine triphosphate (8-oxo-dGTP), 8-oxo-20-deoxyadenosine triphosphate (8-oxo-dATP), and 2-hydroxy-20-deoxtadenosine triphosphate (2-hydroxy-ATP) to corresponding monophosphates, which cannot be assembled in the DNA by polymerases [41, 80]. In 2008, Pursell et al. [81] reported that 8-oxo-dGTP exists in some rat tissues at levels that are potentially mutagenic; therefore, these data suggest that oxidized dNTP precursors could generate mutagenesis in vivo and consequently promote mitochondrial dysfunction. In addition, it was reported that a pathogenic variant of Polγ, which is present in patients with progressive external ophthalmoplegia (PEO), increases 8-oxo-dGTP misincorporation, observation that establishes a relationship between the oxidative lesions and increased mtDNA damage observed in other models with this pathogenic version, and misincorporation of oxidized nucleotides [82]. In summary, although sanitation of premutagenic free nucleotides is not properly a DNA repair mechanism, its participation prevents the formation of mismatches in mitochondrial genome and therefore reduces the probability of mutagenesis.

#### *4.6.2 mtDNA degradation*

Compared to nuclear genome, mitochondrial genomic material has a remarkable advantage about DNA damage and repair, its redundancy, consisting of hundreds to thousands of copies per cell. Due to this characteristic, mitochondria

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

 can dispose of a considerable fraction of mtDNA, where its repair capabilities were exceeded; however, it does not compromise organelle functions, and this is not an option for nucleus, where the diploid genome cannot be submitted to degradation without affecting the cellular homeostasis [3]. It is thought that after mtDNA degradation, the lost molecules are restored by mitochondrial genome turnover, a process that was first described several decades ago [83] (**Figure 2**). There is a wide body of evidence that supports this hypothesis of mtDNA degradation after unrepairable insults; for instance, it was observed that when one of the initial steps of the BER repair pathway is inhibited by methoxyamine drug, the increase of incidence of oxidative and alkylating damage enhanced the mtDNA degradation [84]; additionally, through qPCR analysis, it has been shown a mtDNA amount decrease after persisting exposure with the oxidizing agent hydrogen peroxide [85, 86]. Furthermore, the absence of mutation fixation after persisting cell treatment with alkylating agents which have a high mutagenic potential suggests that due to the lack of mechanisms for repairing bulky lesion, the mtDNA could be selectively degraded and to prevent further modifications [87]. Nowadays, it is not completely clear how the mitochondrion degrades its damaged DNA; however, it has been recently determined that endonuclease G (EndoG) has an important role in mtDNA depletion, since it promotes cleavage of mtDNA as a response to oxidative and nitrosative stress, action that subsequently generates an upregulation of mtDNA replication as an indirect outcome [88]. This evidence is supported by the fact that endo G is the most abundant and active nuclease within mitochondria, and it has a preference on oxidized DNA harboring single-strand breaks or distorted DNA product of crosslinking agents to exert its endonuclease activity in vitro [89], also it has been reported that this nuclease preferentially cleaves 5-hydroxymethylcytosine an oxidized product of 5-methylcytosine [90]. In conclusion, despite that additional research is needed to elucidate the whole mechanisms and elements that participate in mtDNA degradation, this pathway emerges as a unique and mitochondrial specific method to maintain DNA integrity.

#### **Figure 2.**

*mtDNA degradation and mitophagy. (A) Damaged mtDNA (yellow circles) can be selectively degraded inside mitochondria, thus keeping "healthy" mtDNA (green circles), then this can replicate to re-establish mitochondrial genome homeostasis. (B) If the mtDNA is severely damaged and the repair mechanism is surpassed, injured mitochondria can be selectively degraded by the formation of an autophagosome and subsequent fusion with lysosomes [91]. On the other hand, the mtDNA lesions can also trigger cell apoptosis.* 

#### *4.6.3 Mitochondrial clearance, dynamics, and apoptosis*

 In general terms, autophagy is a highly conserved degradative mechanism used by cells to maintain homeostasis [92]. This is a finely regulated process that takes part in cell growth, development, and in the maintenance of an equilibrium between synthesis, degradation and recycling of cellular elements including whole organelles [11]. There is a specialized sub pathway of autophagy, which is specifically involved in degradation of damaged and dysfunctional mitochondria, and this procedure is known as mitophagy or mitochondrial clearance. Although mitophagy can emerge as a programmed cellular event, like the one that is observed during erythroblast maturation in order to generate mature red blood cells lacking mitochondria [11], it has been proposed that mitophagy could participate in the elimination of organelles harboring low levels of DNA damage stress. On the other hand, when the DNA lesions are too many to handle with mtDNA repair mechanism or by mitochondrial clearance, the cellular response could trigger apoptosis [93], therefore the choice of which pathway must be used depends on the degree of DNA damage (**Figure 2**). In accordance with the previous mechanism, Suen et al. [94] observed selectively degradation by mitophagy of organelles harboring deleterious COXI mutations after overexpressing the protein Parkin, which translocated to affected mitochondria and induced autophagic elimination, thus this selection enriched cells for nonmutated mtDNA and restoring cytochrome c oxidase activity [95].

 It appears that mitophagy is closely associated with mitochondrial dynamics processes: fission and fusion [96]. Fusion is the joining of two organelles to form one, this mechanism allows mitochondria to distribute mtDNA and to replenish it when is damaged, therefore safeguarding mtDNA integrity and protecting it from mutations [97]. On the other hand, fission is the division of a single organelle to create two, this process is very important to cellular viability, it contributes to symmetrical distribution of mitochondria during mitosis, and promotes the removal of lesioned organelles by partitioning the damaged elements (like mtDNA) to a derived mitochondria that can fuse to a healthy one with the intention of recovering functionality or to be degraded by mitophagy. Therefore, mitochondrial removal by mitophagy is preceded by mitochondrial fission, which is capable of dividing the organelle into smaller pieces to be degraded easily [98]. When mitochondrial clearance, fusion, or fission are dysfunctional, the cells could be severely affected, since it has been observed that in these situations, an increase in mtDNA instability and generation of neurodegenerative, cardiovascular, and age-related diseases were obtained [99].

#### **5. mtDNA repair, diseases, and aging**

 Mitochondrial diseases are a heterogeneous group of illnesses affecting multiple organs and leading to eventual degeneration and in some cases premature death. These affectations have origin in mutations on mtDNA, which are generated by errors during DNA replication, exogenous sources, and ROS; however, mitochondrial dysfunction may also arise from mutations in nuclear genes which encode proteins with mitochondrial function, involved in several processes like biogenesis, transcription, replication, mitochondrial dynamics, and mtDNA repair, among others. Of interest, neurodegeneration is a prevalent trait in mitochondrial diseases, maybe because the brain needs a higher demand of energy in comparison with other tissues [11]. On the other hand, there is a large body of evidence that underscores the relationship between mitochondrial disorders and aging; however, there is still

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

controversy about whether these mutations in the mtDNA are the product of agerelated disorders or they are themselves the cause [100].

About the genes involved in mtDNA maintenance, it has been well established that failure of the mtDNA repair pathways may promote diseases and age-related disorders in humans [11, 28]; in addition to mutations, the reduction of mtDNA copy number has also been associated with neurodegeneration, aging, diabetes, and cancer [101]. For example, it has been observed that the lack of proofreading activity of Polγ in mice generates multi-systemic disease and phenotypes resembling to premature aging [102], furthermore, over 200 mutations in POLG have been associated with mitochondrial diseases, these POLG-related disorders can be classified into five main phenotypes of neurodegeneration: Alpers-Huttenlocher syndrome (AHS), childhood myocerebrohepatopathy spectrum (MCHS), myoclonic epilepsy myopathy sensory ataxia (MEMSA), ataxia neuropathy spectrum (ANS), and PEO [28], besides, mutations in Twinkle helicase often causes infantile onset spinocerebellar ataxia (IOSCA), which usually appears in early childhood [103]. Other mtDNA repair elements, such as APTX and TDP1, implicated in SSBR, are related with the generation of ataxia with ocular motor apraxia (AOA1) when are mutated [10, 104]. Also, defects in the proteins CSA and CSB, implicated in the possibly mitochondrial DNA repair transcription coupled-NER pathway, are related with the development of progressive cerebellar pathology [105]. Furthermore, alterations in fusion, fission, or mitophagy processes due to mutations in the proteins involved generate mtDNA instability, which in turn may induce neurodegenerative, cardiovascular, and age-related diseases [99], such is the case of MFN2, which is implicated in mitochondria fusion, and its alteration lead to organelle fragmentation and causes axonal Charcot-Marie-Tooth disease (CMT2A) [106], also mutations in OPA1, lead to optic atrophy, affectation that can be accompanied with hearing loss and ophthalmoplegia [107]. Additionally, mutations in DNA2 and mitochondrial genome maintenance exonuclease 1 (MGME1) nucleases are implicated in ophthalmoplegia, myopathy, and mtDNA depletion [108, 109]. In conclusion, the importance of mtDNA maintenance lies in the observation that when the repair elements are affected, or the mechanisms exceeded, the risk of disease development increases, thus the understanding of these alterations may shed light for clinical targets to prevent diseases or treat them.
