Beyond base excision repair: an evolving picture of mitochondrial DNA repair

Abstract

Mitochondria are highly specialised organelles required for key cellular processes including ATP production through cellular respiration and controlling cell death via apoptosis. Unlike other organelles, mitochondria contain their own DNA genome which encodes both protein and RNA required for cellular respiration. Each cell may contain hundreds to thousands of copies of the mitochondrial genome, which is essential for normal cellular function - deviation of mitochondrial DNA (mtDNA) copy number is associated with cellular ageing and disease. Furthermore, mtDNA lesions can arise from both endogenous or exogenous sources and must either be tolerated or corrected to preserve mitochondrial function. Importantly, replication of damaged mtDNA can lead to stalling and introduction of mutations or genetic loss, mitochondria have adapted mechanisms to repair damaged DNA. These mechanisms rely on nuclear-encoded DNA repair proteins that are translocated into the mitochondria. Despite the presence of many known nuclear DNA repair proteins being found in the mitochondrial proteome, it remains to be established which DNA repair mechanisms are functional in mammalian mitochondria. Here, we summarise the existing and emerging research, alongside examining proteomic evidence, demonstrating that mtDNA damage can be repaired using Base Excision Repair (BER), Homologous Recombination (HR) and Microhomology-mediated End Joining (MMEJ). Critically, these repair mechanisms do not operate in isolation and evidence for interplay between pathways and repair associated with replication is discussed. Importantly, characterising non-canonical functions of key proteins and understanding the bespoke pathways used to tolerate, repair or bypass DNA damage will be fundamental in fully understanding the causes of mitochondrial genome mutations and mitochondrial dysfunction.

Keywords: DNA replication and recombination; DNA synthesis and repair; genome integrity; mtDNA.

Figure 1. Gene ontology enrichment analysis of DNA repair proteins in the mitochondrial proteome reveals BER and DNA recombination as enriched biological processes

(A) Protein products of genes annotated with the ‘DNA repair’ gene ontology were screened against the curated IMPI. Forty candidate DNA repair proteins were identified in the mitochondrial proteome representing multiple DNA repair pathways. Black circles represent circular mtDNA in a mitochondrion (orange/pale orange). (B) GO enrichment analysis of the 40 candidate genes was performed using clusterProfileR to identify associated biological processes [33]. Analysis reveals BER, DNA recombination, DSB repair and DNA replication as the four most enriched biological processes.

Figure 2. Multiple fates for damaged mtDNA

(A) The mtDNA (blue circles) encounter several base lesions including oxidation, alkylation and deamination which are primarily repaired by BER. In contrast, DSBs are repaired either by MMEJ or trigger DNA degradation by a yet unknown mechanism. HR repair of protein–DNA cross-links requires both homologous template sequences and RAD51 to repair damage. DSBs may also be processed and repaired by HR. (B) During replication, abasic sites generated through BER processing are either repaired by TLS using gap filling activity of POLγ or are targeted for degradation. Lesions present in mtDNA during replication may lead to replication stalling and generation of further DNA breaks which can be repaired by MMEJ or potentially using the non-canonical replication restart functions of RAD51C and XRCC3 (CX3) alongside RAD51. Purple circle represents TWINKLE helicase and Blue rectangles represent mtSSB loading on the displaced strand, red arrow indicates direction of DNA synthesis. Red text indicates key proteins identified in each process. Abbreviations: mtSSB, mitochondrial single-stranded binding protein; TLS, translesion synthesis.