Repair of persistent strand breaks in the mitochondrial genome

Abstract

Oxidative DNA damage has been attributed to increased cancer incidence and premature aging phenotypes. Reactive oxygen species (ROS) are unavoidable byproducts of oxidative phosphorylation and are the major contributors of endogenous oxidative damage. To prevent the negative effects of ROS, cells have developed DNA repair mechanisms designed to specifically combat endogenous DNA modifications. The base excision repair (BER) pathway is primarily responsible for the repair of small non-helix distorting lesions and DNA single strand breaks. This repair pathway is found in all organisms, and in mammalian cells, consists of three related sub-pathways: short patch (SP-BER), long patch (LP-BER) and single strand break repair (SSBR). While much is known about nuclear BER, comparatively little is known about this pathway in the mitochondria, particularly the LP-BER and SSBR sub-pathways. There are a number of proteins that have recently been found to be involved in mitochondrial BER, including Cockayne syndrome proteins A and B (CSA and CSB), aprataxin (APTX), tryosyl-DNA phosphodiesterase 1 (TDP1), flap endonuclease 1 (FEN-1) and exonuclease G (EXOG). These significant advances in mitochondrial DNA repair may open new avenues in the management and treatment of a number of neurological disorders associated with mitochondrial dysfunction, and will be reviewed in further detail herein.

Fig. 1

Nuclear and mitochondrial DNA repair shares common proteins. However not all nuclear DNA repair pathways are present in the mitochondria. However the BER pathway has a high degree of conservation between the two organelles, with most of the mitochondrial BER proteins, isoforms of nuclear relatives. Abbreviations are as follows: base excision repair (BER), miss match repair (MMR), nucleotide excision repair (NER), non-homologous end joining (NHEJ) and homologous recombination (HR).

Fig. 2

Resolution of persistent mitochondrial single strand breaks. A strand break with blocking groups at one or both exposed ends is unable to be repaired by simple SP-BER. The detection of these lesions may rely on more than one enzyme and potentially involves PARP, CSB or TFAM. The detection method may influence the type of lesion processing, either damage reversal, if a specific enzyme such as APTX or TDP1 are able to resolve the lesion, or damage excision, a more generic pathway that excises the DNA damage using the LP-BER pathway. In the mitochondria LP-BER dependant multi nucleotide excision appears to be driven by EXOG as part of an APE1 complex however the presence of FEN-1 and DNA2 in the mitochondria suggests a secondary LP-BER pathway, potentially to excise lesions resistant to EXOG activity. After the lesion has been resolved nucleotides are inserted by polymerase γ and the phosphodiester backbone re-ligated by ligase 3.

Fig. 3

DNA–AMP complex formation and the resolution of the lesion in the nucleus. The AMP intermediate is formed when the DNA ligase encounters a strand break with a blocked 3′ end. The ligase protein does not recognize that this substrate is unligateable and begins ligation but is unable to complete the ligation because of the incompatible 3′ end. Ligation is prematurely terminated leaving a 5′-AMP residue. The break site is potentially recognized by PARP in the nucleus, signaling the recruitment of an APE-1 complex, consisting of ligase 3, XRCC-1 and the 5′-AMP resolving protein aprataxin. Aprataxin rolls back ligation, processing the 5′ AMP and leaving a SSB. This SSB is then able to be processed by BER.